Open Source Software
"Never trust salespeople who don't use their own products."
- Preface, The Practice of System and Network Administration by Thomas A. Limoncelli & Christine Hogan

Below is software that I use or have used before. I believe all of these projects to be usable replacements of their commercial counterparts (if a commercial equal exists). Most of these apps I have used for quite a while before adding them to this list. I consider them to be (or near) stable and of good quality.

I currently am trying to make donations to some of my favorite projects to show my appreciation for the developer's hard work. I am more partial to projects that work on multiple platforms or are platform independent, since I work on multiple platforms and it's nice to use the same apps on each.

New York Times Firefox Ad - PDF
Closeup of my name in the ad :) - here
Wikimedia Foundation featured comment (yess) - here
X-mas card from Wikimedia Foundation - here
Example of me using Dia - here

Thus far I have donated to:
Apache Software Foundation - 1 donation
Audacity - 1 donation
Azureus - 1 donation
BitTorrent - 1 donation
Calibre - 1 donation
CDex - 1 donation
ClamWin Antivirus - 1 donation
Comix - 1 donation
CyanogenMod - 1 donation
Dev-C++ - 1 donation
DOSBox - 3 donations
FileZilla - 2 donations
FixParts - 1 donation
Free Software Foundation - 1 donation
GIMP - 2 donations
GNOME - 5.5 donations
HardInfo - 1 donation
HSQLDB - 1 donation
Hydrogen - 1 donation
Internet Book List - 1 donation
KDE - 3 donations
Memtest86 - 1 donation
Mozilla/Spread Firefox - 4 donations
Notepad++ - 1 donation
OpenBSD/OpenSSH, etc - 3 donations
OpenOffice - 4 donations
OpenShot - 2.5 donations
SETI Spy - 1 donation
SourceForge - 1 donation
TightVNC - 1 donation
Tomato Firmware - 1 donation
VideoLAN - 1 donation
VisualBoyAdvance - 1 donation
Wikimedia Foundation (Wikipedia) - 7.5 donations (1 in 2014)
Xiph.Org - 1 donation
Zim - 1 donation
ZSNES - 1 donation

^(1 donation = $10)^
External link to Yahoo! Finance Currency Conversion - finance.yahoo.com/m3?u

Instant Messaging/Chat
Linux/Win32
Gaim (now named Pidgin)
Gaim-Encryption (now named Pidgin-Encryption)
Pidgin/Finch - www.pidgin.im
Pidgin-Encryption - pidgin-encrypt.sf.net

Linux Only
Irssi - www.irssi.org

Win32 Only
HydraIRC - www.hydrairc.com

Multimedia
Linux/Win32
Audacity - audacity.sf.net
Avidemux - fixounet.free.fr/avidemux
Cdrtools (Cdrecord) - cdrecord.berlios.de/old/private/cdrecord.html
EasyTAG - easytag.sf.net
GCstar - www.gcstar.org
gPodder - www.gpodder.org
HandBrake - www.handbrake.fr
VLC Media Player - www.videolan.org/vlc
Linux MultiMedia Studio (LMMS) - lmms.sf.net
Hydrogen - www.hydrogen-music.org
Xvid - www.xvid.org
Nosefart - nosefart.sf.net
Sidplay2 - sidplay2.sf.net
MikMod - mikmod.raphnet.net
MilkyTracker - www.milkytracker.net
Miro - www.getmiro.com
Mixxx - mixxx.sf.net
SoX - sox.sf.net

Linux Only
AcetoneISO - www.acetoneteam.org
Audacious - audacious-media-player.org
Banshee - www.banshee-project.org
Brasero - projects.gnome.org/brasero
Cheese - projects.gnome.org/cheese
Festival - www.cstr.ed.ac.uk/projects/festival
F-Spot - www.f-spot.org
gtkpod (Banshee provides this program's functionality)
guvcview - guvcview.berlios.de
K3b - k3b.plainblack.com
OpenShot - www.openshotvideo.com
Qmmp - qmmp.ylsoftware.com/index_en.php
rubyripper - code.google.com/p/rubyripper
SoundConverter - soundconverter.berlios.de
thoggen - www.thoggen.net
X MultiMedia System (XMMS) (discontinued)
xvidcap - xvidcap.sf.net

Win32 Only
CDex - cdexos.sf.net
Greenshot - www.getgreenshot.org
VirtualDub - www.virtualdub.org
InfraRecorder - infrarecorder.sf.net
CamStudio - www.camstudio.org
MediaCoder (no longer open source)
Nightingale - www.getnightingale.com
OpenPandora - openpandora.googlepages.com
WinCDEmu - wincdemu.sysprogs.org
Songbird (replaced by Nightingale)

Office
Linux/Win32
AbiWord - www.abisource.com
Aspell - aspell.sf.net
Calcoo - calcoo.sf.net
Calibre - www.calibre-ebook.com
Dia - www.gnome.org/projects/dia
DocSearcher - docsearcher.henschelsoft.de
FreeMind - freemind.sf.net
GPL Ghostscript - www.cs.wisc.edu/~ghost
LibreOffice - www.libreoffice.org
MSGViewer - www.freecode.com/projects/msgviewer
OpenOffice (succeeded by LibreOffice)
RSSOwl - www.rssowl.org
Truth Table Solver - truthtablesolve.sf.net
wikidPad - wikidpad.sf.net
XMind - www.xmind.net
Zim - www.zim-wiki.org

Linux Only
Gnumeric - www.gnome.org/projects/gnumeric
GnuCash - www.gnucash.org
KOffice - www.koffice.org
KchmViewer - www.kchmviewer.net
Calctool (Gcalctool) - calctool.sf.net
KPDF (replaced by Okular)
GtkSpell - gtkspell.sf.net

Win32 Only
PDFCreator - sourceforge.net/projects/pdfcreator
GraphCalc - gcalc.sf.net
Sumatra PDF - blog.kowalczyk.info/software/sumatrapdf/index.html

Boot disks/Boot utilities
N/A
BackTrack - www.backtrack-linux.org
Memtest86 - www.memtest86.com
Memtest86+ - www.memtest.org
Darik's Boot and Nuke - dban.sf.net
Knoppix - www.knoppix.org
Parted Magic - www.partedmagic.com

Web applications
N/A
Alfresco - www.alfresco.com
BBClone - www.bbclone.de
Coppermine Photo Gallery - www.coppermine-gallery.net
Drupal - www.drupal.org
Joomla! - www.joomla.org
jsFiddle - www.jsfiddle.net (not sure if open source, but very useful)
MathJax - www.mathjax.org
Matt's Whois - www.mattsscripts.co.uk/mwhois.htm
MediaWiki - www.mediawiki.org
My Calendar - www.fuzzymonkey.net/software/calendar
PhpBB - www.phpbb.com
phpDVD - ugo.scarlata.it/?pid=phpdvd
phpMyInventory - phpmyinventory.sf.net
PHPSysInfo - phpsysinfo.sf.net
quizzy - quizzy.sf.net
Webmin - www.webmin.com
WordPress - www.wordpress.org
SSHTools - www.sf.net/projects/sshtools

File Sharing/File Transfer
Linux/Win32
BitTorrent (no longer open source)
Azureus/Vuze (still open source, but commercialized & bloated)
FileZilla - filezilla.sf.net
JDownloader - www.jdownloader.org

Linux Only
gFTP - gftp.seul.org
Monsoon (Transmission is more mature)
Transmission - www.transmissionbt.com
rTorrent - libtorrent.rakshasa.no

Win32 Only
WinSCP - www.winscp.net

File/System Utilities
Linux/Win32
B5I2ISO - developer.berlios.de/projects/b5i2iso
FixParts - www.rodsbooks.com/fixparts
KDiff3 - kdiff3.sf.net
mdf2iso - mdf2iso.berlios.de
Nrg2Iso - gregory.kokanosky.free.fr/v4/linux/nrg2iso.en.html

Linux Only
alien - www.kitenet.net/~joey/code/alien
Beagle - beagle-project.org
convmv - www.j3e.de/linux/convmv
Filelight - www.methylblue.com/filelight
FUSE - fuse.sf.net
GNOME Commander - www.nongnu.org/gcmd
GParted - gparted.sf.net
HardInfo - hardinfo.berlios.de
htop - htop.sf.net
inxi - code.google.com/p/inxi
KDirStat - kdirstat.sf.net
Krusader - krusader.sf.net
Midnight Commander - www.ibiblio.org/mc
Parted - www.gnu.org/software/parted
ps3 - user.tninet.se/~uhu537u/ps3.html
ncdu - dev.yorhel.nl/ncdu

Win32 Only
WinDirStat - windirstat.sf.net
7-Zip - www.7-zip.org
WinMerge - www.winmerge.org

Emulation
Linux/Win32
Atari800 - atari800.sf.net
Basilisk II - basilisk.cebix.net
Caprice32 - www.caprice32.cybercube.com
ColEm - fms.komkon.org/ColEm
DeSmuME - www.desmume.org
Dolphin - www.dolphin-emu.com
DOSBox - dosbox.sf.net
Dynagen - www.dynagen.org
Dynamips - www.ipflow.utc.fr/index.php/Cisco_7200_Simulator
FCE Ultra (succeeded by FCEUX)
FCEUX - www.fceux.com
FS-UAE - www.fs-uae.net
Fuse - fuse-emulator.sf.net
Gens (succeeded by Gens/GS)
Gens/GS - info.sonicretro.org/Gens/GS
GNS3 - www.gns3.net
Hatari - hatari.berlios.de
Hu-Go! - www.zeograd.com
JPCSP - www.jpcsp.org
MEKA - www.smspower.org/meka
Mupen64Plus - code.google.com/p/mupen64plus
openMSX - openmsx.sf.net
PCSX2 - www.pcsx2.net
PCSX-Reloaded - pcsxr.codeplex.com
Raine - rainemu.swishparty.co.uk
Reality Boy - www.goliathindustries.com/vb
ScummVM - www.scummvm.org
Snes9x - www.snes9x.com
Stella - stella.sf.net
VICE - www.viceteam.org
VirtualBox - www.virtualbox.org
ZSNES - www.zsnes.com
VBA-M - www.vba-m.com
Virtual Jaguar - icculus.org/virtualjaguar
VisualBoyAdvance (succeeded by VBA-M)
Yabause - www.yabause.org

Linux Only
Wine - www.winehq.com
DOSEMU - www.dosemu.org
FreeDOS - www.freedos.org
GFCE Ultra (merged into FCEUX)
Open VM Tools - open-vm-tools.sf.net
SDLMAME - rbelmont.mameworld.info/?page_id=163
Wiithon - https://launchpad.net/wiithon

Win32 Only
WinUAE - www.winuae.net
Multiple Arcade Machine Emulator (MAME) - www.mame.net
MAME32 (now called MameUI)
MameUI - www.mameui.info
Ootake - www.ouma.jp/ootake
VirtuaNES - virtuanes.s1.xrea.com:8080
AppleWin - applewin.berlios.de
Handy - handy.sf.net
VI Plug-in SVMotion (functionality included in VCenter 4.x)

Development
Linux/Win32
GCC - gcc.gnu.org
Free Pascal - www.freepascal.org
RHIDE - www.rhide.com
OpenJDK - openjdk.java.net
SCons - www.scons.org
Komodo Edit - www.activestate.com/komodo_edit
Scintilla - www.scintilla.org
Code::Blocks - www.codeblocks.org
NetBeans - www.netbeans.org
Eclipse - www.eclipse.org
CodeLite - www.codelite.org

Linux Only
Anjuta - anjuta.sf.net
KDevelop - www.kdevelop.org

Win32 Only
Dev-C++ - www.bloodshed.net
DJGPP - www.delorie.com/djgpp
Crimson Editor - www.crimsoneditor.com

Text Editors
Linux/Win32
Nano - www.nano-editor.org
Vim - www.vim.org
Emacs - www.gnu.org/software/emacs

Linux Only
gedit - gedit.sf.net

Win32 Only
Notepad++ - notepad-plus.sf.net

Games
Linux/Win32
0A.D. - www.wildfiregames.com/0ad
Abuse - abuse.zoy.org/
Angband - www.rephial.org
Armagetron Advanced - www.armagetronad.net
AssaultCube - assault.cubers.net (not entirely open source)
Atomic Tanks (Atanks) - atanks.sf.net
Barrage - lgames.sf.net/index.php?project=Barrage
Battle for Wesnoth - www.wesnoth.org
Battle Tanks - btanks.sf.net
Blob Wars: Metal Blob Solid - www.parallelrealities.co.uk/projects/blobWars.php
BZFlag - www.bzflag.org
Chromium B.S.U. - www.reptilelabour.com/software/chromium
Circus Linux! - www.newbreedsoftware.com/circus-linux
DarkPlaces - www.icculus.org/twilight/darkplaces
EDuke32 - www.eduke32.com
Enigma - www.nongnu.org/enigma
Extreme Tux Racer - www.extremetuxracer.com
ezQuake - ezquake.sf.net
Freedoom - www.nongnu.org/freedoom
FooBillard - foobillard.sunsite.dk
Frotz - frotz.sf.net
Gargoyle - www.ccxvii.net/gargoyle
Globulation 2 - www.globulation2.org
GLtron - www.gltron.org
Goblin Hack - goblinhack.sf.net
GPL Arcade Volleyball - gav.sf.net
Hedgewars - www.hedgewars.org
IceBreaker - www.mattdm.org/icebreaker
Star Control 2: The Ur-Quan Masters - sc2.sf.net
Frozen Bubble - www.frozen-bubble.org
Lincity - lincity.sf.net
Liquid War - www.ufoot.org/liquidwar
MegaMek - megamek.sf.net
Mirror Magic - www.artsoft.org/mirrormagic
Moria - www.beej.us/moria
NetHack - www.nethack.org
Neverball - icculus.org/neverball
Nexuiz - www.alientrap.org/nexuiz
OpenArena - www.openarena.ws
OpenLieroX - openlierox.sf.net
PokerTH - www.pokerth.net
PrBoom - prboom.sf.net
Project: Starfighter - www.parallelrealities.co.uk/starfighter.php
Risk - jrisk.sf.net
Rocks'n'Diamonds - www.artsoft.org/rocksndiamonds
SolarWolf - www.pygame.org/shredwheat/solarwolf
SuperTux - supertux.berlios.de
Tile World - www.muppetlabs.com/~breadbox/software/tworld
Tremulous - www.tremulous.net
Warmux - www.gna.org/projects/warmux
Warzone 2100 Resurrection - www.wz2100.net
Wolfenstein 3-D Redux - wolf3dredux.sf.net
wxSand - www.piettes.com/fallingsandgame
XBill - www.xbill.org
X-Moto - xmoto.tuxfamily.org
XWelltris - xnc.dubna.su/xwelltris
Zod Engine - zod.sf.net

Linux Only
Atlantik (no longer maintained)
Blob Wars: Blob and Conquer - www.parallelrealities.co.uk/projects/blobAndConquer.php
GTetrinet - gtetrinet.sf.net
KDE Games - www.kde.org/kdegames
Kollision - games.kde.org/game.php?game=kollision
Koules - www.ucw.cz/~hubicka/koules/English/koules.html
Pingus - pingus.seul.org
PySol - www.pysol.org
Random Shooter - www.parallelrealities.co.uk/projects/randomShooter.php
Virus Killer - www.parallelrealities.co.uk/projects/virusKiller.php

Win32 Only
Artificial Planet -  aiplanet.sf.net

Servers/Server Utilities
Linux/Win32
Apache HTTP Server - httpd.apache.org
Apache Tomcat - tomcat.apache.org
Apache Derby - db.apache.org/derby
Squid - www.squid-cache.org
MySQL - www.mysql.com
MySQL Administrator - www.mysql.com/products/tools/administrator
phpMyAdmin - www.phpmyadmin.net
BIND DNS Server - www.isc.org/sw/bind
Firebird - www.firebirdsql.org
FlameRobin - www.flamerobin.org
SQuirreL SQL - www.squirrelsql.org
rsync - www.samba.org/rsync
SQLite Database Browser - sqlitebrowser.sourceforge.net

Linux Only
Samba - www.samba.org
OpenSSH - www.openssh.com
Openfiler - www.openfiler.com
vsftpd - vsftpd.beasts.org
ProFTPD - www.proftpd.org
PXELINUX - syslinux.zytor.com/wiki/index.php/PXELINUX
Dnsmasq - www.thekelleys.org.uk/dnsmasq/doc.html

Email Clients
Linux/Win32
Mozilla Thunderbird - www.mozilla.org/products/thunderbird
YPOPs! - www.ypopsemail.com
MrPostman - mrpostman.sf.net

Linux Only
Evolution - www.gnome.org/projects/evolution

Graphics
Linux/Win32
Sodipodi (replaced by Inkscape)
Gimp - www.gimp.org
MyPaint - mypaint.intilinux.com
Pngcrush - pmt.sf.net/pngcrush
Inkscape - www.inkscape.org
XSane - www.xsane.org
Cornice - wxglade.sf.net/extra/cornice.html
Pencil - www.pencil-animation.org
ImageMagick - www.imagemagick.org
Luminance HDR - qtpfsgui.sf.net

Linux Only
Evolvotron - www.bottlenose.demon.co.uk/share/evolvotron
Comix (development halted)
MComix - mcomix.sf.net (maintained version of Comix)
feh - linuxbrit.co.uk/feh
KolourPaint - www.kolourpaint.org
Fotoxx - kornelix.squarespace.com/fotoxx
Kooka (no longer maintained)
Skanlite
Xara Xtreme - www.xaraxtreme.org

Win32 Only
PNGShot - pngshot.sf.net
Ascgen dotNET (ascgen2) - ascgendotnet.jmsoftware.co.uk
CDisplayEx - cdisplayex.sf.net

Networking/Security
Linux/Win32
Nmap - www.insecure.org/nmap
GNU Privacy Guard (GPG) - www.gnupg.org
Ipcheck.py (functionality is built into Tomato firmware)
Ethereal (replaced by Wireshark)
Wireshark - www.wireshark.org
TightVNC (forked to TigerVNC)
TigerVNC - www.tigervnc.org
Clam AntiVirus - www.clamav.net
PuTTY - www.chiark.greenend.org.uk/~sgtatham/putty
WPA Supplicant - hostap.epitest.fi/wpa_supplicant
Angry IP Scanner - www.angryziber.com/ipscan
ntop - www.ntop.org
Mozilla Firefox - www.mozilla.org/products/firefox
cURL - curl.haxx.se
Ettercap - ettercap.sf.net
OpenSSL - www.openssl.org
ophcrack - ophcrack.sf.net
ipcalc - www.jodies.de/ipcalc
Hyperic - www.hyperic.com
John the Ripper - www.openwall.com/john
wol - www.sf.net/projects/wake-on-lan
Steghide - steghide.sf.net
BitPim - www.bitpim.org
Snort - www.snort.org

Linux Only
Tripwire - www.tripwire.org
rdesktop (replaced by FreeRDP)
NdisWrapper - ndiswrapper.sf.net
FreeNX - freenx.berlios.de
FreeRDP - www.freerdp.com
Cheops-ng - cheops-ng.sf.net
Asterisk - www.asterisk.org
TrixBox (Asterisk@Home) - asteriskathome.sf.net
Knowlan - www.enderunix.org/knowlan (alternative: arpscan)
whois - www.linux.it/~md/software
Tomato Firmware - www.polarcloud.com/tomato
PowerTOP - www.lesswatts.org/projects/powertop
Galeon (replaced by Epiphany)
OpenIPMI - openipmi.sf.net
Kismet - www.kismetwireless.net
Zenoss - www.zenoss.com
ScanSSH - www.monkey.org/~provos/scanssh
w3m - w3m.sf.net
Remmina - remmina.sf.net
Seahorse - projects.gnome.org/seahorse
Sleuth Kit (and Autopsy) - www.sleuthkit.org
OSSEC - www.ossec.net
OpenVAS - www.openvas.org

Win32 Only
Windows Privacy Tools (WinPT) - winpt.sf.net
WinPcap - www.winpcap.org
ClamWin Antivirus - www.clamwin.com
Program Killer - progkill.sf.net
Blat - www.blat.net

Mac OS X Only
OSXvnc - www.sf.net/projects/osxvnc

Web Development
Linux/Win32
Nvu (replaced by KompoZer)
KompoZer - www.kompozer.net (perhaps replaced by BlueGriffon)
Linklint - www.linklint.org
Bluefish - bluefish.openoffice.nl

Shells/Terminals
Linux Only
Eterm - www.eterm.org
Bash - www.gnu.org/software/bash/bash.html
Konsole - konsole.kde.org
ttyrec - 0xcc.net/ttyrec/index.html.en
YaKuake - yakuake.uv.ro
Screen - www.gnu.org/software/screen
cool-retro-term - https://github.com/Swordfish90/cool-retro-term

Win32 Only
Cygwin - www.cygwin.com
Poderosa - en.poderosa.org

Screen Savers
Linux/Win32
electric sheep - www.electricsheep.org

Linux Only
XScreenSaver - www.jwz.org/xscreensaver
ASCIIQuarium - www.robobunny.com/projects/asciiquarium/html

Win32 Only
Really Slick Screensavers - www.reallyslick.com
ZMatrix - zmatrix.sf.net

Distributed Computing
Win32 Only
SETI Driver (no longer appears to be active)
SETI Spy (no longer updated, sadly the author passed away. my condolences)

Science
Linux/Win32
Stellarium - www.stellarium.org
Celestia - www.shatters.net/celestia

Linux Only
KStars - edu.kde.org/kstars