Luke Skywalker - I'm going to go with POTF2 Bespin (Saga was too posed to suit me, though you combine his articulation with POTF2's sculpt/pose and I'd be one happy campter).
Han Solo - POTJ Bespin Capture version is AWESOME. Articulation, sculpt, holster feature, and binders.
Princess Leia - I'm gonna go with POTJ Deluxe or POTJ Bespin Escape. I'm not real keen on many of the Leia's though.
Chewie - Hands down Saga Cloud City Capture is the best... Articulation, great accessories, great sculpt... Just great.
Lando - Has to be POTJ Bespin Lando. Just wish he had more articulation and I'd be content with him.
Obi-Wan Kenobi - I like Naboo Obi-Wan with his robes. That's just me. Nice Vanilla robed Obi...
Yoda - The Saga Yoda w/Youngling is great, but I'd like to see new Yoda's in every incarnation with soft goods accessories.
Darth Vader/Anakin - Right now I still am partial to the POTF2 removable helmet version but I'll make an "ultimate" one someday that will be better than anything Hasbro's done (But cobbled of their own parts). What they should've done in the first place.
R2 - Easily POTF2 Commtech R2 wins hands down. Awesome sculpt, deco, and articulation PLUS a great accessory.
3PO - While Matt's MMC 3PO is worthy, I have to say that Saga Deluxe 3PO takes the cake. THAT is why Hasbro should be commended for their ability to do great sculpts. Too bad they don't do great in the other areas. It's the best scupted Saga figure IMO though.
Emperor/Palpatine - I'm going with Saga Chancellor Palpatine on this one. Impressive sculpt, good articulation, interlocking fingers, liverspots, and a nice outfit. He's a grand figure for a grand character.
Qui-Gon - I'm gonna say his "best" was the POTJ moisture farmer outfit figure, but I've yet to see a truly "great" one that can hold his sabre multiple ways and be well posed. Too bad considering what a good character he was.
To me these are the only "main" characters really. The rest strike me as secondary, and then background.