This is a compilation list featuring useful reference sites, quality programs and tools, and services that are ideal for the indie developer on a tight budget.

Bolded items are programs worth checking out first. This is based on my opinion, as well as others but they are very nice and do what they do very well.

If someone finds any dead links, errors, unforgivable omissions ( laugh ), or something else, please post away.

2D:
Paint.NET - free paint program that should get you by for most things
GIMP - free and powerful paint program
Project Dogwaffle - "natural" paint and animation program...lots of unique features not commonly found in other paint programs
ArtRage - another “natural” paint program
Paintshop Pro - paint program...commercial product
Deep Paint - freeware paint program
openCanvas - paint program...commercial product
Flash SWF Tools - lots of SWF Flash tools and programs, logo and menu creation programs
Inkscape - SVG/vector graphics editor
Moho (Anime Studio) - 2D bones based animation
Texture Maker - general purpose seamless texture generator
Wood Workshop - procedural seamless wood texture generator...free
Genetica - procedural seamless texture generator
Crazy Bumps - bakes normal maps from 2D art assets
Caustics Generator - water texture generator...free
Graffiti Creator - online graffiti generator...free and new commercial version
PNG Gauntlet - fantastic PNG converter & optimizer
GUIGenie - GUI builder...free
Cut-Sew - 2D vector graphics and cuttable designs from the creator of fragMotion (see below)

3D:
Blender - free and powerful 3D editor...a MDL7 export script is available.
Wings 3D - modeling/rendering with FBX import/export but no animation or bones support...free
Silo - modeling/rendering...like Wings only better and commercial
CB Model Pro - intuitive, Zbrush-like program for organic modeling and painting. OBJ export and free after email registration. Ideal for high poly models for normalmaps
Milkshape - modeling/animation editor featuring a large number of model format exports
trueSpace 7.6 - modeling/animation/rendering...freeware
AC3D - easy on the eyes UI...your standard modeling app
Misfit Model 3D - open source modeling program
Daz Studio - Poser-like figure creation and similar license restrictions apply. Nice for 2D renders or 2D animations...free
MakeHuman - 3D figure creation
Truebones.com - inexpensive motion capture...if you can get it to work (try fragMotion), this is both a steal and an animation paradise
DeleD - level and model editor hybrid...free version
Ultimate Unwrap - model unwrapping and UVs....3DGS export
UVMapper Classic - OBJ model unwrapping and UVs..free version
fragMotion - character animation program...fantastic and powerful....low cost....3DGS MDL, X, and FBX (in development) export
LifeForms Gamepak 1 - premade game animations
Mixamo - rapidly create, rig and animate unique characters
Nem's Terrain Generator
Terragen - photorealistic scenery rendering
World Machine - procedural terrain generator w/erosion...free version

Other:
Indie Tools - a list of tools/programs to make game creation easier
Inno Setup - installer..free
CreateInstall - installer..free version
NSIS - installer...free
Molebox - non extracting file packer
TalkToMe - lipsyncing SDK for 2D or 3D
Audacity - audio editor..free
Kristal Audio Engine - Cubase clone...free and open source
Divx - video codec...high compression & quality..free for noncommercial use
XVid - superior open source video codec....will open Divx files.....free to use
TMPGEnc - video convertor
Fraps - video capture...free version
Taksi - FRAPS knockoff...open source video capture...free
OBS Studio - free and open source software for video recording and live streaming
Virtualdub - powerful video compression app...free
VLC Media Player - open source video/audio player...free
dBPowerAMP - audio convertor with nice UI...lots of codecs...free
Exact Audio Copy - free audio ripper..the best in the world
LAME MP3 Encoder - the best MP3 encoder...use with Exact Audio Copy
Font Creator - a nice TTF creator, editor, and viewer
SubtitlesK5ky - add subtitles to AVI..free
RAD Video Tools - video/image/sound convertor & tweaker...free
Open Office - MS Office knockoff....graphics, spreadsheets, powerpoint, word processing and more.....free
Celtx - pre-production script writing tool...free
7-Zip - file archiver/compression...free
TikiWiki - free
osCommerce - open source online shop e-commerce software...free
SmartFTP - free FTP client
Core FTP LE - free FTP client
Website Baker - open source PHP website software...free
WordPress - free blog software, "5-minute installation"
Photobucket - online image hosting
Bittorrent - useful for large resource and demo dispersement..eliminates webhosting and bandwidth consumption...free
Pidgin - multi-platform, multi-protocol, instant messaging client; formerly known as Gaim...free
Trillian - multi-protocol, instant messaging client...free
Open Clip Art Library - vector based....read license...free
1001 Free Fonts - free fonts

Reference and organizations:
Anatomy Atlases - large selection of anatomy atlases
3D Science - medical models and images...prices vary...some freebies
Human Photo References for 3D Artists and Game Makers - this site contains nudity...you've been warned
More human photo references and environmental textures - this site contains nudity...you've been warned
Morgue File - royalty free photo reference site...commercial usage permitted
Public domain art links - just what it says
Google Earth - satellite photos of just about everywhere...broadband required....free
LipSync - tutorial
Low poly modeling and texturing tutorials
Onnovanbraam blueprints - vehicles & people
Vehicle blueprints
ANIMAX - free textures
Turbo Squid - 2D/3D resource buy/sell site
CafePress - service that allows you to sell merchandise based on your company/game...free
IGDA - International Game Developer's Association
DevMaster - game developer sites
Gamasutra - free registration is mandatory to read articles on this game developer/news site
Gamedev - popular game developer information site
Indiegamer Forums - discuss everything related to indie life and more with real indies
Shareware Directories - listing of most of the major shareware distributors
PAD file information - PAD files are used to expediate online, automated information gathering

IndieDB Game Engines List - huge list of game engines

Here's another list on the Gamedev forum. There's a bit of overlap, but it's biased more towards programmers: http://www.gamedev.net/community/forums/topic.asp?topic_id=324643

Here's yet another list containing hundreds of freeware/shareware programs: http://www.snapfiles.com/freeware/freeware.html

***UPDATED: March 31st, 2019***


My User Contributions master list - my initial post links are down but scroll down page to find list to active links