Funniest moment in all of Doctor Who?
Personally I loved the first half of Tom Baker's run due to how serious and adult the tone was for the most part. It did, for me, contain the funniest moment in all of Doctor Who, and that was in the episode "The Android Invasion" (either Part 3 or 4).
The Doctor runs past an android Benton and he says "Don't shoot Benton, I'm one of you!". Benton doesn't shoot.
Another Doctor (the android copy version) runs in and says the exact same thing, the same way.
Benton fires several shots into The Android Doctor's torso which have absolutely no effect.
Android Doctor: "Satisfied?".
It probably would not have been nearly as funny without Tom Baker's excellent delivery, which sounds merely annoyed that he was just shot, and the insinuation that even the android copies of The Doctor and Benton have the same dynamic as their real life counterparts.