General Programming
Beagle Bros Online Museum	If you missed the heydays of the Beagle Bros, you missed a lot. These guys made software for the Apple II series back in the eighties, and could pack everything you would need for your computer onto one 140K floppy disk, with room left over for games. Sadly, when the Apple II went the way of the dodo, they closed shop, and all that's left is this museum.
The WOZ's Home Page	The home page of the one and only Steve Wozniak, co-founder of Apple Computer, and one of the most brilliant hardware hackers to ever grace the face of the Earth. He doesn't do much coding or hardware these days; nowadays he spends a lot of time teaching, but even so, he's still the Woz.
Interface Hall of Shame	Is your favorite program here? We hope not! This site parades what you already knew --- that most software is unusable junk! If you're a programmer, you should study this site, because if you don't, you'll be doomed to repeat these horrid mistakes...
Virtual Network Computing (VNC)	Finally, something cool from AT&T. This software is totally free and lets you use any computer from any other computer on the same network, regardless of which operating systems each runs. If you need to use computers remotely, you need VNC.
Graphics Programming
Chris Hecker's Home Page	Lots of information about 3-D texture mapping. Chris is the author of a well-known set of articles in Game Developer Magazine that were the first to truly expose the nebulous subject of 3-D perspective texture mapping, and his home page has lots of info related to these (now out of print) articles.
FreeType Project	The FreeType Project aims to produce the first fully open-source TrueType font renderer.
GamaSutra: Feature Articles	Helpful articles on a wide variety of 3-D graphics programming topics.
GamaSutra: OpenGL Texture Objects	A useful introduction to the use of texture objects in OpenGL, which allow much better texture management than the simple traditional initial-texture-upload.
Paul Heckbert's Home Page	Paul Heckbert is the father of 3-D texture mapping, being the first to discuss it in depth in his 1984 Doctoral Thesis. His home page has lots of neat documentation on the topic, but it can be very mathematically dense.
Data Structures and Algorithms
NIST's Dictionary of Algorithms & Structures	The complete dictionary of every common data structure, algorithm, and problem in computer science. Even though it's an overview, it can be really helpful if you can't remember the difference between a Hamming distance and a ham sandwich.
Anythings Home Page	The Anything is the world's slickest hierarchical data structure. These versatile structures can store anything, including other Anythings. Too bad their web site seems to always be down.
Data Compression Links	Lots of links to everything related to the world of data compression.
L4Ka	L4Ka is a project to build the world's smallest microkernel operating system. This is a beautiful design, and makes monolithic systems like Windows, MacOS, and Linux look downright pathetic by comparison.
Internet and World Wide Web
Perlfect Solutions: Perl scripts	Perlfect Solutions offers a variety of top-quality free Perl scripts for various web needs. I use their code on my own sites, because while I could write the code myself, why should I when they've already done such a good job?
The W3C	The W3C is the World Wide Web Committee --- these guys officially decide how the World Wide Web works. If you need info about how the Web works, this site is the horse's mouth.
The W3C: The HTTP Protocol	HTTP is the network protocol that underlies the World Wide Web. If you need to know how it works, this is the official source.
The W3C: HTML 4.01	HTML is the language in which web pages are written. This page is the official source for HTML documentation, but it assumes you know how to read XML DTDs, so if you don't, you'll be very lost.
DevEdge Online	Netscape's developer documentation. Although this information is occasionally outdated, and even occasionally apocryphal, it's still the best documentation outside of the W3C, and the HTML Tag Reference is worth a visit all by itself.
Linux
Kernel.org	The primary source for new versions of the Linux kernel.
slashdot.org	I don't go here much anymore, but it's not a bad site for Linux-related news. Unfortunately, these days, the signal-to-noise ratio requires limit theory to be measured, but occasionally Slashdot stumbles onto good news.
PalmOS
PalmOS Docs	Official programming documentation from Palm.
Falch.net	Occasionally helpful programming documentation for the PalmOS.
Darrin Massena's Tools and Articles	Massena was one of the first to crack the silence around the PalmOS, and although his site is getting a little outdated, it's still an invaluable resource to every PalmOS programmer.
Windows Programming
Microsoft: Globalization	Microsoft's own documentation on writing international-enabled software.
Ghost Installer	A powerful, free install program generator for Windows.
UPX Home Page	UPX is a free tool for compressing Windows executables to save disk space. They still run, and never know that they've been shrunk.