Can't decide on one. Thrill of the Hunt, Lost and Found, Megatron Rising and A Bridge too Close were my highlights though.
Either Lost & Found, Mission Accomplished or Transform & Roll Out Part 3. (Prime vs. Starscream, FTW) EDIT: Stupid anti-abbreviater.
Transform and Roll out 3-parter, Along came a spider, Megatron Rising, A Bridge. And my fav is whatever the Episode the had Starscream repeatedly getting killed and tossed of a cliff.
Fistful of Energon isnt the best but man did it set me ablaze with all of the neato Sergio Leone in gags.
Autoboot Camp. One of the funniest half hours of TF animation ever, with great characterization for two major characters, as well as Sentinel Minor. It is also one of the few times my brother has watched a TF show the whole way through because he could rather than because he happened to be there at the time and he outright said he liked it, which is really saying something for him.
Not counting the season finales, I would have to go with Autoboot camp. Besides being fun, they gave us a good look at Cybertron.
Transformers and Rollout 1-3 Lost and Found Thrill of the hunt Sound and Fury Megatron Rising Pt 1 &2 Garbage in Garbage out Autoboot Camp A Bridge to close Part 1 and 2.