Oh god my friend you have openned up a huge Can of worms
Okay here it goes
Autobots
Fortress Maximus (comic version most notably....killed Galvatron)
Optimus Prime (Awesome from the show, one of the few who actually came off better than he initially did in the comic)
God Ginrai (i.e. Powermaster Prime who was the BEST Prime ever as seen in Marvel Comics....he killed Unicron in issue 86 sacrificing himself in the process)
Rodimus/Hot Rod
Outback is a great little toy
Nightbeat is a cool character (he is an autobot detective and was featured in a film noir story in the comic)
Prowl (horrendous on the show, great in the comic...lived till the bitter end ironically in Marvel, double crossed by Bludgeon)
Decepticons
Galvatron
Scorponok/ Black Zarak
Megatron
Starscream
Soundwave/ Soundblaster
Cyclonus
Hellbat
Bludgeon
Honorable Mentions
Grimlock (comic Marvel)
Blaster (comic Marvel)
Minerva
MetalHawk