The SRD lists the core skills, as well as the skills added by Expanded Psionics Handbook (Autohypnosis, Knowledge (psionics), Psicraft, Use Psionic Device). There is also, in the SRD but hidden, the Control Shape skill used by lycanthropes.
But some supplements add new skills. The Iaijutsu Focus skill from Oriental Adventures is fairly well-known. Tome of Battle’s Martial Lore is another Spellcraft analogue, and Tome of Magic’s Truenaming is the skill that fuels the worst class in the game. And a friend just came across the bizarre Handle Monstrous Spider skill from Dungeon vol. 84, which I’d never heard of before.
Since the factotum class gains all skills as class skills, unusual skills can sometimes be relevant to one. Does anyone know of a really thorough listing of skills, including Dragon and Dungeon magazines and all Wizards of the Coast supplements for 3.0e and 3.5e? Primarily interested in totally-new skills, rather than new Craft, Knowledge, Perform, or Profession skills (though when they get special rules, as with Craft (poisonmaking), or most Knowledge skills, that’s more interesting).