I believe that the briefcase being searched for in Pulp Fiction holds the diamonds from the Reservoir Dogs heist. Originally the briefcase in PF was going to use diamonds, but this was changed to avoid similarities to the previous film, and there are two characters named 'Vega' who were originally going to be brothers (and Tarantino has never conclusively stated that they ain't) This is tied in to another theory that they actually take place either on the same day or very very close to each other.
I do not, categorically and completely, believe that there is a special dormitory for Head Boys and Girls in Hogwarts that Dumbledore uses to set up students who have feelings for each other but won't admit it. I waver on the 'Lupin is obsessed with chocolate' thing. While I don't think it has special significance, he does say that it helps with bad feelings and he does seem to be depressed a lot of the time, so maybe he turns to it for comfort. There's a couple of other smaller things I usually accept as canon as well, but nothing major.
In Merlin I like the fanon that Merlin and Morgana have a little bit of chemistry, but that's mostly from the way the two actors play it rather than anything else.
I obviously think that Sheldon from TBBT have some form of autism/Aspergers. He has almost every single sign for gods' sake!
I accept most of what The Last Days of Foxhound says, even a lot of the stuff proved untrue by canon, just because I enjoy TLDOF more than I enjoy MGS.
I assume that Ron Stoppable's Actuary father set up an account to deal with his massive Bueno Nacho welath.
I do tenuously hold to the theory that Azula has raped or attempted or wanted to rape several character in A:TLA
I believe quite a few Teen Titans theories. Beast Boy and Raven have some sort of feelings for each other, Jump City is called 'Jump City' and is located in California, Robin is an insomniac and Dick Grayson, Raven was on her period during the movie...
I like fanon. It's fun.