Abraham Lincoln's Assassination -- comprehensive and even-handed.

The Academic JFK Assassination Web Site --  remarkably fair-minded and comprehensive, included many worthwhile, hard-to-find documents and articles.

Bad Astronomy -- Phil Plait's site tackling many forms of astrophysical misconception, including the Moon Landing Hoax and "Face on Mars" theories

Committee for the Scientific Investigation of Claims of the Paranormal (CSICOP) -- leading organization of "skeptics" committed to debunking paranormal and illogical beliefs. Site includes articles from their magazine Skeptical Inquirer. 

Crank Dot Net -- directory of sites on conspiracy theory and other fringe beliefs, created by a skeptic.

DIsinformation -- a self-consciously "hip" pro-conspiracy site. 

Fortean Times -- web site of British magazine on c.t.'s and other weird or alternative beliefs. Occasionally skeptical, done with an unusual sense of intellectual seriousness. 

MUFON -- UFO research group, generally believing. Go here to report a UFO sighting.

Museum of Hoaxes

Nixon Era Times -- lots of Watergate information, promoting the "silent coup" theory that the CIA did in Nixon.

Public Eye -- website of Political Research Associates, run by anti-conspiracism activist Chip Berlet

Public Information Research

Steamshovel Press -- web site of a St. Louis-based c.t. magazine that seems to go for the wildest and most comprehensive theories it can. Seems almost aimed at the c.t. hobbyist and, while laced with humor, does not seem to be a joke. Read with caution.