Quite enjoyed these:
* Rodimus, Ultra Magnus, Springer, Blaster + Dinobots vs Galvatron, Cyclonus, Sourge/Sweeps, Soundwave, Abominus + Predaking (Season 3, Call of the Primatives) - Really enjoyed the animation and the huge roll call, and also because the Autobots was fighting a losing battle. Not sure why they were fighting over a dead moon, but some senseless violence is always welcome
* Generic Autobots + Doublecross vs Snapdragon, Apeface, Combaticons + Terrorcons (The Headmasters, Death of Ultra Magnus) - Sixshot riling up the Decepticons was awesome, and not the best, but Doublecross' fight was funny
I really enjoyed that fight for some reason. I think it's because I watched it as a kid and prior that fight, my only other TF-exposure was G1 Season 1 & 2 which did not have that sort of Japanese violence (or J-rock, which sounded pretty cool to me as a kid).
I have one that strongly comes to mind:
* Cyclonus & Scourge vs Autobot Headmasters (TF The Headmasters) - Cannot recall the exact episode(s), but I really did not enjoy the way Cyclonus & Scourge were portrayed as bumbling comic relief and continuously got their arses handed back to them.