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Necessities

Essential

Google
Your guide to the dense jungle that is the Internet.
foobar2000
A very good and non-bloated audio player.
Winamp
My second favorite audio player.
Opera
My favorite web browser.
Firefox
My second favorite web browser.
Google Chrome
A browser that is currently in beta. It's looking interesting. I particularly like its intuitive and non-intrusive in-document search.
XPize
Makes your XP shine like a neutron star.
Launchy
An application launcher.

Reference material

hyperdictionary
What does 'defenestration' mean?
Online Etymology Dictionary
What's the story behind the word 'campus'?
HowStuffWorks
How do UPC bar codes work?
pinouts.ru
Can DVI carry analog signals?
The Phrontistery
What's an exequy?
Unwords
Isn't a hallucidation a contradiction in terms?
Wikipedia
What are hot Jupiters?

Editors

TextPad
A very good text editor. It does line numbering, keyword highlighting, and regex searching. It doesn't do code folding.
MetaPad
MetaPad replaces Notepad.

Utilities

SIW
Tells you everything about your computer.
Microsoft PowerToys
Small programs that make life in Windows XP happier (I like CmdHere.exe and PowerCalc.exe).
Sysinternals Suite
Small programs that make troubleshooting your computer easier.

Gaming

Flash games

3D Logic
Make non-overlapping colored paths on a cube's six faces.
Gridlock
Help a brick get out of its room.
The Hapland series
Make things work and then escape through a portal.
Planarity
Untangle a planar graph.

Other games

Ballance
Awesome ball game with neat music.
Cave Story
A sweet 2D side-scrolling action-adventure game. You find yourself underground, in a cave system. Be sure to pick up the Deluxe edition, as it contains the OST as MP3s, a level editor, and a small game called Ikachan.
Elasto Mania
An unrealistic (and therefore fun) 2D motocross game. See Moposite for replays and high scores.
Enigma
A ball game. I mean, a puzzle game. I mean, a dexterity game. I mean, an action game.
N
You play a ninja who has to escape rooms by doing what ninjas do best (escaping rooms).
Narbacular Drop
The precursor to Valve's Portal.
Neverball
A ball game. See Neverball Hall of Fame for replays and high scores.
Shyguy's Cave of Death
Pick up coins and avoid everything else.
Simon Tatham's Portable Puzzle Collection
A lot of small, fun puzzle games. My favorites are Inertia and Net.
Sokoban++
A good clone of the classic Sokoban warehouse game. Push boxes into designated areas.
StepMania
An emulator (sort of) for DDR. Hit arrows in sync to the music's beat. See Bemanistyle for music.
TrackMania Nations
A free racer. If you like Nations, why don't you consider buying TrackMania United and its prequels? See TMX for more goodies.
The Ur-Quan Masters
A mind-blowing science fiction game. UQM is Star Control 2 for modern computers, but it has some extra features like voice acting. Be sure to use The Ultronomicon in your adventures around the Milky Way.

Emulation

EDuke32
An emulator for Duke Nukem 3D. Hail to the king, baby!
Gens
The de facto Sega Genesis emulator.
PlayGuy
The best GameBoy emulator that I've found.
Tile World
An emulator for Chip's Challenge. (You need the file chips.dat to play it.)

Gaming help

GameFAQs
Helpful user-submitted walkthroughs, maps, and in-depth FAQs for a lot of games.

Gaming encyclopedias

Encyclopedia Twinsunica
[Little Big Adventure] Don't get too close to the Supergros.
The Ultronomicon
[Ur-Quan Masters] The game doesn't have any form of a tutorial, so you might want to use the Ultronomicon extensively.
Halopedia
[The Halo series] Did you realize that Graveminds speak in trochaic heptameter?
Combine OverWiki
[The Half-Life series] Did you know that the voice actor of Alyx Vance, Merle Dandridge, also supplies Alyx' face?
Encyclopedia Hiigara
[The Homeworld series] Did you know that the Khar-Toba was only one of many exile ships?

People

Friends

I know them very well and talk to them frequently.

Alex Spurling
A software developer in England.
Even Alander
A student of 3D design with whom I live.

Others

I think these people are interesting.

Eric S. Raymond
Maintainer of the Jargon File.
Jakob Nielsen
A bi-weekly column dealing with web design.
Jeff Dee
An artwork designer known for his work in the AD&D books, as well as an outspoken atheist.
John Walker
Founder of Autodesk. His site is huge and contains all manner of interesting things.
Mindstalk
A self-described polymath.
Paul Graham
Paul Graham is an excellent essayist.
Phil Plait
Also known as the Bad Astronomer.
Sam Hughes
Things Of Interest, and the title doesn't lie.
Stephan T. Lavavej
A software developer at Microsoft. Reading his site was what pushed me into learning HTML and creating a web site of my own.

Cerebal

Science

Charles Darwin Online
Contains all things Darwin.
Kunstformen der Natur
Insanely high resolution images of the pages from this famous book by Ernst Haeckel. (The title is German and means "Artforms of Nature".)
talk.origins
Explains what evolution is all about, and explores evolution/creationism confrontations.
Ebon Musings
Reflections beneath the Milky Way.
Rationally Speaking
The web site of Massimo Pigliucci.
RichardDawkins.net
Contains all things Richard Dawkins (and more).
Pharyngula
The blog of PZ Myers, a developmental biologist at the University of Minnesota, Morris.

Books

LibriVox
A library of free audio books.
Project Gutenberg
A library of books in the public domain.

Audio

Music

Airbase
Has an online store of MP3 songs. My Life and Schizofren are awesome.
Aura
Has lots of free songs. Breathing Silence and Naked Angel are magical.
Aural Planet
Awesome downtempo trance. Blue Water Cave and Have You Ever Been are sweet.
Labworks
Labworks makes mostly vocal trance (mmm, female voices). My favorites are Summerbreeze (Aura Remix) and Two Worlds (Airplay Edit).
Lynne Music
Bjørn Lynne is best known for composing the music to the Worms games and his site offers a selection of songs for download.
NiCe Music
Has lots of hours-long mixes. Yummy.
Shadow of the Beat
Makes drum-and-bass-ish music.
Sonic Mayhem
Makes action-type music.
Xerxes Music
Downtempo electronic-type music.

Remix sites

VGMix
Hosts lots of quality remixes for game music.
Hybridized
Has tons of hour-long mixes. Great stuff for having in the background when working.

Collection sites

Galbadia Hotel
Look no further for game OSTs and anime music.

Podcasts

Point of Inquiry
PoI interviews prominent intellectuals, philosophers, and scientists.
The Thomas Jefferson Hour
A weekly podcast dealing with Thomas Jefferson and his views. The show is made by a scholar impersonating Jefferson being interviewed.

Visual

Exploration

Google Earth
Lets you explore the Earth.
World Wind
Also lets you explore the Earth, but with more statistics.
Celestia
Lets you explore the universe. Check out The Celestia Motherlode for things with which to populate that virtual universe.

Art

deviantART
Lots of amateur art. You can buy prints (I have four).
Bathsheba Grossman
Grossman makes mathematical art (I own the Large Scale Model).
Art of Greg Martin
Makes neato space pictures.

deviantART

alexiuss
Draws majestic characters and apocalyptic scenery.
Artgerm
Draws wonderfully pretty ladies.
daggerpoint
Draws super hero-type women and plain pretty women. (Not all SFW.)
DKF
Mostly space renderings.
mr-mister
Draws strong women. Sexy!
Philipstraub
Awesome vistas.
PolishPanties
Draws awesome manga, but unfortunately the gallery is tiny.
reiq
Draws mostly NSFW women.
spirapride
Draws various things, including pretty women, Final Fantasy, and Ninja Gaiden.

Images

Visible Earth
Our planet is grand and beautiful.

Video

Beyond Belief I and II
Two very interesting annual symposia on science and religion. The first is vastly superior to the second, but Peter Atkins made the second one not suck. (I can't wait for the third.)
Loading-Ready-Run
Canadian sketch comedy group.
the show with Ze Frank
A discontinued show about news and stuff. (Ze Frank is my Dear and Glorious Leader!)
Growing Up in the Universe
A children's lecture on evolution by natural selection, I mean by Richard Dawkins.

Various

Physics

Animating Fracture
I, for one, want to shoot steel balls through walls of ceramic and PVC.
Gravitas
I, for one, want to hurl galaxies at each other.
Falling Sand Game
I, for one, want to watch sand and other miscellaneous particles fall.
Ronald Fedkiw's simulations
I, for one, want to serve water from a hollow Buddha statue.

Online comics

Daily

Cyanide and Happiness
A stick-figure comic with revoltingly funny jokes. Therefore, only mature minds should read it.

MWF (or other three-days-a-week schedule)

Cectic
Skepticism in comic form.
Decorum
Geeky comic about life, the universe, and subatomic particles.
Penny Arcade
Canonical reading for any gamer.
The Warehouse
OONTZ-OONTZ-OONTZ-OONTZ
xkcd
Some nights typing "*hug*" just doesn't cut it.

Weekly

Simulated Comic Production
Cautionary tales.

Haphazard

Dresden Codak
What you get when you are high on science.
f8d
Minimalist musings on various things of interest.
LegoRobot
Weird and incredibly hilarious stories about unstable people.
Miscellanea
Flow diagrams and funny slides.
Nearing Zero
Jokes for nerds, jokes for nerds.
Pixel
What if pixels had philosophy?
Subnormality
Crazy stuff in everyday life.
VG Cats
Funny cats making comments on games.

Frozen

Big Science and Proverbs
Two discontinued comics by Albert Sweigart which ran in The Daily Texan, a student newspaper of The University of Texas at Austin. I think almost all of the Big Science ones are hilarious. Proverbs occasionally falls flat.
Concerned
A comic about an alternate story for Half-Life 2 (sadly discontinued).