Fight! Super...: Glaze (Blades), because the manga portrayed him in a way that was most accurate to the way that his original G1 toy tech specs bio describes him (i.e. Gung-Ho kickyoass action junkie).
2010: Rodimus Convoy... just cos in the manga he wasn't the whinging self doubter that we saw in the anime/cartoon series.
The☆Headmasters: Sixshot. He's a ninja, what's not to like?
Super God Masterforce: Ginrai - I got to watch Masterforce as a youngin' in those Super God-awful dubs, but even then I thought "Optimus Prime" was pretty damn awesome!
Victory: Machtackle. The episode where Mach and Tackle switch places is one of my favourites.
Zone: Dai Atlas. He gets criticised a lot, but I think he's a really interesting character. The Marvel TFU profile for Optimus Prime says that as part of his weakness, he would be a better military commander if he were more ruthless, but then he wouldn't be Optimus Prime... well, here's an Autobot commander who's more than willing to be utterly ruthless in battle. A lot of Japanese fans hate him for that, but I think it's what makes him a more interesting and unique character.
Return of Convoy: Super Megatron. They should make a Generations toy based on this dude.
Operation Combination: Can't comment as I've never read it
For me it's about what makes a character stand out to me.
Hubcap.
Artfire and Stepper.