My own top three...
1. Perceptor is definitely my favorite Autobot.

I've always had a big soft spot for the brainy/nerdy characters in any given universe (mainly because *I'm* a bit of a nerd...)
I like the way he has a quiet, unflappable sort of courage (in contrast to most of the other Autobots, who tend to be rather energetic gung-ho types, though that's fun also). He reacts to most things with the same sort of cheerful matter-of-fact adaptability, whether it's getting arrows shot at him by the natives, dueling Soundwave with a giant pencil(!), or trying to negotiate with a ranting, rusting Megatron.
I also can empathize with getting all excited about sharing some new bit of knowledge you find interesting, using vocabulary you find perfectly normal and understandable, only to have someone yawn from boredom and demand you speak English. He certainly handles it with greater aplomb than I did as a kid (and my friends were even less snotty about it than most of the Autobots).
Finally, he's got a cool altmode ('Scope-Cam!), an equally neat robot mode (yay, giant shoulder-mounted laser cannon - that's a lot of firepower for a brainy type...), and a pleasant accent.
2. On the flip side, Starscream is my favorite Decepticon. Much as I usually hate jumping on the bandwagon, he's just so irresistably entertaining to watch chewing the scenery.
Whether he's being a slimy bastard, an arrogant egotist, a snivelling coward, or leaping impatiently before he looks (and sometimes all of that at once), he steals almost every scene he's in. It's fun watching him get one over on Megatron and the other Decepticons, and it's equally fun watching him get smacked for it when Megatron gets back in control again.
Plus, the Autobots should be thankful for Starscream. Without him throwing a spanner into the works for the Cons on a regular basis, they'd have lost a lot more often.

3. This is a bit trickier, since there's many other characters I find appealing, but... I think maybe I'd have to pick Silverbolt.
You kind of have to feel sorry for the guy. He's stuck having to herd the Autobot equivalent of a bunch of smart-mouthed teenagers, *and* he's afraid of heights (thus proving that the universe has a twisted sense of humor).
Yet he manages to be responsible, compassionate, have a good deal of common sense, and can be delightfully crafty and sharp-witted when the situation calls for it. And brave as well... anyone can be courageous about something they're not afraid of, but having to deal with something that scares you silly? I'm acrophobic myself, and I avoid being more than a few feet off the ground whenever possible. :X I'd certainly be in trouble if I was saddled with a flying altmode.
I'd post an Honorable Mention list, but it'd be rather long. It's what I like most about Transformers, I think - there's so many fun and appealing characters.