Dai's List of Conworlding/Worldbuilding Links:

Note: I don't vouch for the accuracy of any of these.

Physical World/Universe/Sciency Things:
Planet Designer: Calculator for stars and planets. Hard science
http://www.johnbray.org.uk/planetdesigner/

Astro: Calculator for Stellar & Planetary Orbits, Planets and Satellite Orbits, Rotational Habitats, and Asteroid Crater Sizes. Originally aimed at the Hard SF RPG 2300 AD, but the science is good.
http://www.bumply.com/astro.html

StarGen: Random generator for star systems and planets. Also has a downloadable version.
http://fast-times.eldacur.com/StarGen/RunStarGen.html

World Generation: Another randomized generator, aimed at the Traveller RPG, but still useful.
http://www.trisen.com/sol/static/wg/wg.html

Plan a Planet Orbiting a Main Sequence Star
http://web.archive.org/web/20030218125318/www.geocities.com/Area51/Corridor/8611/mseqstar.htm

Hard SF Tools
http://web.archive.org/web/20070823084250/http://www.geocities.com/Area51/Corridor/8611/hard-sf.htm

Antimatter Calculator: Just for fun, calculates the energy from matter/antimatter explosions.
http://www.edwardmuller.com/right17.htm

Church of Climatology: http://www.spinnoff.com/zbb/viewtopic.php?t=34650

Creating an Earthlike Planet: http://www-users.york.ac.uk/~fc503/geoff/worldkit.html

Geoff's Climate Cookbook: http://www-users.york.ac.uk/~fc503/geoff/climate.html

Fundamentals of Physical Geography: http://www.physicalgeography.net/fundamentals/contents.html

The Geography Site: http://www.geography-site.co.uk/index.html

World Builder's: CSU's Worldbuilding Course
http://www.world-builders.org/

An Atlas of the Universe: http://www.atlasoftheuniverse.com/

Star Data Pages: http://www.alcyone.de/SIT/

Planetary Fact Sheets:
http://nssdc.gsfc.nasa.gov/planetary/planetfact.html

Ecology
Introduction to the Biosphere, from Fundamentals of Physical Geography: http://www.physicalgeography.net/fundamentals/chapter9.html

Drake Equation: Calculator for the Drake Equation.
http://www.activemind.com/Mysterious/Topics/SETI/drake_equation.html

Holly Lisle's Rollicking Rules of Ecosystems:
http://hollylisle.com/fm/Articles/rules-of-ecosystems.html

Holly Lisle's Holly Lisle's Shopping List for Better BEMs:
http://hollylisle.com/fm/Articles/bem-shopping-list.html

Astrobiology Magazine
http://www.astrobio.net/astrobiological_news.php

Major Biomes of the World:
http://www.runet.edu~swoodwar/CLASSES/GEOG235/biomes/main.html/

Maps
Fractal World Generator: makes fractal maps.
http://donjon.bin.sh/world/

Holly Lisle's Maps Workshop -- Developing the Fictional World through Mapping:
http://hollylisle.com/fm/Workshops/maps-workshop.html

Fantasy
Holly Lisle's Fantasy Is Not for Sissies: Real Rules for Real Worlds:
http://hollylisle.com/fm/Articles/rules-for-better-fantasy.html

30 Days of World Building:
http://www.web-writer.net/fantasy/days/index.html

Magical World Builder's Guide: Guide to building fantasy worlds.
http://www.web-writer.net/fantasy/

10 Steps to Creating Realistic Fantasy Animals
http://www.elfwood.com/farp/thewriting/animalash/animalash.html

Patricia C. Wrede's Fantasy Worldbuilding Questions: also useful for non-fantasy cultures.
http://www.sfwa.org/2009/08/fantasy-worldbuilding-questions/

Cultural/Ethnology Resources

The Zaharam-Chapelle-Parunas Ethnographical Questionnaire (Thank you Tom Chapelle!)
http://bethisad.com/conculture/questionnaire.htm

The Importance of Food: Aimed at RPGs, but touches on an aspect of conworlding that I haven't really seen talked about much here.
http://ptgptb.org/0024/food.html

Worlds
The Speculative Dinosaur Project: no K-Pg extinction event.
http://www.unet.univie.ac.at/~a0000265/Spec/index.html

Orion's arm Universe Project: Huge galaxy spanning hard SF world building project.
http://www.orionsarm.com/

Furaha: http://members.casema.nl/gertvandijk/

Epona: http://www.eponaproject.com/Epona_Home.html

Planetocopia: Variations on Earth.
http://www.worlddreambank.org/P/PLANETS.HTM

Snaiad: http://www.nemoramjet.com/snduterus.html

Collected Links:
Hobgoblin.net's World Building resources for writers: http://www.hobgoblin.net/modules/mylinks/viewcat.php?cid=7

Future Studies: Transhumanist resources.
http://www.aleph.se/Trans/Cultural/Future/

Hard SF: Collection of links and essays about Hard SF.
http://www.hardsf.org/NofrInde.htm

Orion's Arm Links: Orion's Arm is a huge hard SF world building project. These are their world building resources links. There's some overlap with this list.
http://www.orionsarm.com/xcms.php?r=oa-links
World Building Links: http://www.orionsarm.com/xcms.php?r=oa-page&page=gen_worldbuilding_links

World Builder Projects: http://hiddenway.tripod.com/world/

Specfic World's resouces: http://www.specficworld.com/resources/world.aspx

Fantasy World Building Resources: http://www.squidoo.com/fantasyworldbuilding

Assorted Other Useful Resources:
(These are things that I've found interesting/useful.)
Space future: Promoting the human use of space - lost of SF/space information.
http://www.spacefuture.com/directory.shtml

Technovelgy: Collection of SF inventions.
http://www.technovelgy.com/

Maritime knowledge: Useful collection of information if you want details on sailing topics.
http://www.psych.su.oz.au/vbb/woronora/maritime/

1814 Nautical Glossary: What it says - a glossary of nautical terms in use in 1814. http://www.psych.su.oz.au/vbb/woronora/maritime/Glossary.html

1814 Questions for Young Officers: A "test" for young officers on sailing ships - useful if you want details on how sailing ships operate.
http://www.psych.su.oz.au/vbb/woronora/maritime/Questions.html

Lots of online calculators: http://www.csgnetwork.com/converters.html

Science calculators: http://www.csgnetwork.com/scienceconverters.html

Mapping Tool:
http://www.giss.nasa.gov/tools/gprojector/download_win.html

Gravitational Simulator:
http://www.orbitsimulator.com/gravity/articles/what.html