I mostly liked the character-centered episodes, which let Bots and Cons who didn't get much spotlight in the Marvel comics shine. Some of my favourites:
-Golden Lagoon - a pretty good plot device, and also one that shows (in quite a shoehorned way, but nonetheless) the consequences of the Bot/Con war to Earth's nature (then again, "The greatest gift of all" did the same). Plus Beachcomber's starring in it, smoking weed.
-Starscream's Brigade/Revenge of Bruticus: Pretty much a two-part story, one of the few times continuity is maintained in the cartoon. And it's quite a good Bot/Con teamup against the common enemy. Plus Combaticons shining.
-Flight of Flee: A decent episode showing some elements bout what pre-war Cybertron could have been like.
-Megatron's Master plan, aka what happens if the "liberal media" (as Homer would say) starts to paint the Bots as evil and the Cons as good. With hilarious scenes of the casettes in a disco and Ravage stuck in a revolving door.
-Starscream's Ghost, for the huge cast (and kudos for the Battlechargers appearing) and the overall coolness of Starscream, after much-lacked development for the Cons in Season 3.