Links to things which don't fit into the other categories.
Science and Academia
TED: If you haven't heard of TED before, go there now. They provide free special topic lectures from top scientists and thinkers.
EDGE: Another excellent site for science and thinking. Their annual question series contains some of the best writing you'll find on the internet. Free!
The chronicle of higher education. Excellent journal about academia. Many people outside the US don't seem to have heard of it.
Profhacker: This is now a blog within chronicle.com, but is worth having in your RSS feed. Lots of ideas to help you survive academic life.
Science Daily: Science summaries from all fields, free, daily.
NHS Choices: Excellent NHS-run resource which reviews media coverage of new medical discoveries and debunks it. Definitely worth reading; I have it on RSS.
In the Pipeline: Interesting blog about life in medical drug development.
"Should I leave academia?"
Here are some links for anyone who is thinking of a career change.
"100 Reasons not to go to Graduate School". This site does not make comfortable reading for anyone who has devoted a lot of their working life to building an academic career.
also worth reflecting upon:
"It's hard to tell young people that universities recognize that their idealism and energy — and lack of information — are an exploitable resource."
LessWrong: One of the biggest communities of rational people on the internet. Lots of fun.
Overcoming Bias: The site that spawned LessWrong. Also very good.
Eliezer Yudkowsky: An extremely interesting person working on rationality and AI.
ARS Technica: Excellent technology and science articles.
Mac Rumors: Thinking of buying a mac? Better check to see if Apple are about to release a better model!
The daily WTF: How not to program.
Dr Dobbs Journal: Long running excellent magazine about programming.
Bruce Schneier's blog: Excellent resource for computer security news.
The Economist: One of the few paper-based magazines actually worth reading.
FT Alphaville: Irreverent finance blog run by staff at the Financial Times, weighted towards Europe and the UK.
Seeking Alpha: Like most things in finance, 90% full of rubbish, but I've found some real gems here too. It's a sort of community-run finance blog.
Fark.com: I wish the news on TV was more like this.
IO9: Probably the best science fiction website on the internet.
Stepcase Lifehack: Ideas/suggestions for living & working effectively.
Fluent in 3 months: Site & forum about language learning. Quite fun and interesting.
Zen Habits: Slightly hippy website about enjoying life more by changing your habits.
Optimal Charity: If you're going to donate time or money, why not try to do it in a way that achieves the best result possible? You can use sites such as GiveWell to help you find out which charities make the most efficient use of your money.
Internet Radio Stations
Soma FM: 20 unusual radio stations, no adverts, not-for-profit. I recommend 'groove salad'.
Nectarine: Do you pine for the soundtracks of 8-bit computer games, chipmusic and the demo scene? Nectarine has it all. Geeks only.
Dinosaur comics: T-Rex and I have quite a lot in common.
Perry bible fellowship: Bizarre comic, has nothing to do with bibles. Similar to The Far Side.
Moo by Cyriak [not for vegetarians]
Baa by Cyriak [what... what is this???]
I'm a huge fan of Cyriak. He makes everything himself (music, animations, art) at home on an old PC, fuelled only by tea and biscuits and the joy of making weird animations, and he shares most of his work freely with the world (e.g. free/legal MP3s). A true artist.
Banksy: Renegade UK graffiti artist.
Mac Software I like
Newsfire: Beautiful RSS reader, though I've moved to Google Reader.
Comic Life: Extremely fun tool for producing comic books, which can keep PhD students amused for days.
SuperDuper: Life-saving backup utility. Makes a perfect clone of your computer at high speed (via 'Smart update' mode). You can literally plug in a cloned USB drive and boot from it if your main disk fails. Tip: if you use FileVault, set up a 'backup' user account to run it from, and the backup will run even faster.
Skitch: This is a useful program for teachers, lecturers and presenters, which helps you take screenshots and annotate them with cute notes, or put arrows and text bubbles onto photos etc. Review here.
VLC: The best video software available for the Mac, and free.
Cyberduck: Nice FTP/SFTP client, with dashboard app.
Parallels Desktop for Mac: Run Windows on your Mac in parallel with MacOS, at close to full speed.
Excellent Free Games
Allegiance: The most amazing game you've never heard of. It's a real-time strategy game where other human players control the units you give orders to. Microsoft developed this game in the mid-90s, before fast internet connections were easily available in homes. It's a combination of space-ship based first person combat and real-time map based strategy, supporting huge numbers of players. Each team elects 1 commander to issue orders to 5-30 other human players via a large scale map, invests in research and so on. The subscription service wasn't profitable in the late 90s, so Microsoft allowed the game to become freeware. Where it gets fun is that players are free to disobey orders or interpret them as they like, go rogue, elect a new commander at any time. Some of the spaceships require multiple human pilots to control them - imagine being on a 7-person bombing run against an enemy base, with 1 person steering the ship and 6 people firing the cannons! One of the top 5 games I've played in my life.
UFO: AI: A team has reimplemented X-COM in 3D. It's brilliant! A combination of management and turn-based tile strategy. X-COM was one of the most famous games of the 1990s. XCom is also in my top 5 games of all time.
Quake Live: Free internet-based version of Quake 3 (multiplayer FPS), provided by ID Games.
Urban Terror: A free open source multiplayer FPS built on the quake 3 engine. Similar to counter-strike e.g. two teams, terrorists vs counter-terrorists.
Pax Galaxia: Real-time internet-based multiplayer Risk, in space.
World Rebellion: Free internet multiplayer version of Risk.
Toribash: A 3D martial arts physics simulator. Difficult to learn, but very interesting.
Gemcraft Labyrinth: Single player tower defense game.
Amorphous+ Very addictive overhead puzzle-survival game, with really nice ambient jazz music. The game dynamics are extremely interesting.
Brute Wars 2: A sort of battle-themed adventure game, rather like a simple version of Final Fantasy crossed with a card game. Quite fun.
Elements: Excellent online multiplayer card game, a sci-fi relative of 'Magic the Gathering'.
Marvin Spectrum: A test of hand-eye coordination that will drive you insane. My record is something like 240 gates on endless mode.