All are good with the 86 movie Prime VS Megs almost my fave but I have to go with:
1. Optimus Primal VS Megatron (final episode of Beast Machines) they were the only two left on Cybertron and fought each other all over the planet (in the air, on the ground, in the water) And Megs throwing it in Optimus' face by showing up in his Optimal Optimus body was outstanding! EPIC
2. Dinobot VS the entire Predacon crew in "Code of Hero"- probably the most emotionally satisfying bout in the best episode of Beast Wars quote: "I am a warrior, let the battle be joined." That still sends chills down my spine.
3. Depth Charge VS Rampage under the sea in "Nemesis Part 1", the 1st half of the Beast Wars series finale. Very dark and dramatic. Plus I actually thought Depth Charge had stopped Megatron the first time I saw this (I was 13) and then to see his parts float to the surface with Optimus' words =chills. And if that wasn't enough you see the Nemesis rise anyways (which ends the episode).