Megatron's Master Plan- The closest the Decepticons ever came to winning and nearly conquering the Earth... Until Thrust goes and blasts Telatraan-1 inadvertedly saving the Autobots and mankind!
City of Steel- This episode is hilarious it had it all: The Constructicons converting a bunch of taxis into defense drones, Devastator with the King Kong reference swatting Wheeljack's remote controlled helicopters, Soundwave and Megatron sitting at a console using Optimus Prime's severed arm as a defense weapon like they were playing Nintendo. Sideswipe making Starscream say "uncle" and Starscream actually complimenting Megatron for once:
"It sickens me to say it, Reflector, but this one time I have to hand it to Megatron. The place is finally starting to feel like home."
A Prime problem- Lazerbeak pwning Prime! Need I say more? Also I think we got to see what Prime might of looked like had he ever actually gotten drunk... Megatron's Prime clone, calls Ironhide "Bumblebee", starts presing random buttons on Telatraan-1 and tells the Autobots Spike doesn't matter.