The Classic Star Trek Canon
We have a preliminary list of views on some of Classic Star Trek from http://delong.typepad.com/sdj/2007/01/classic_star_tr.html: which parts are canonical and which parts are obvious inferior forgeries:
Genuine and Canonical:
Star Trek II: The Wrath of Kahn
Star Trek IV: The Voyage Home
Star Trek VI: The Undiscovered CountryShore Leave
Mirror, Mirror
The Enterprise Incident
Arena
The Devil in the Dark
Balance of Terror
The Trouble with Tribbles
The Changeling
A Piece of the Action
Charlie X
A Taste of Armageddon
The Menagerie
Space Seed
The City on the Edge of Forever
Amok Time
The Omega Glory
Possibly Canonical, but Subject to Dispute:
The Gamesters of Triskelion
Star Trek: The Animated Series, various episodes
Definitely Heretic:
Spock's Brain (The Rex Momus heresy)
Star Trek I: The Motion Picture (The Bruce Moomaw and Jacob Levy heresy)
Star Trek III: The Search for Spock (the Stoffel and Bruce Moomaw heresy)