As a kid I really liked The Ultimate Doom. And to me, the funniest moments were:

Grimlock: "Me Grimlock not care. Whole planet fall apart... make no difference to me, Grimlock."
Wheeljack: "With you on it?!"
Grimlock: <pause> "Hadn't thought of that..."

And this...
Shockwave: "You cannot escape!" <blasts hole in a wall>
Skyfire: "I can now!"

Now watching it I lawl at the Transformer's use of laser discs. (which at the time was pretty damn funky) -- still no where near as funny as how Optimus Prime's entire core consciousness can fit onto a single floppy disk.

As an adult looking back, my favourite episode would have to be The God Gambit because of the awesome social commentary it makes about religion -- which we won't discuss on the forum, but you get the idea.