I've got a few ideras on this front:
Darth Maul:
The best I have is the version from the Evolution of the Sith 3 pack. I believe he's been repackaged in the current Saga Legends run.
Darth Sidious:
My favorite remains the POTF one though he has limited articulation. The ROTS Black Robed Palpatine is quite good as well and very articulated.
Anakin Skywalker & Darth Vader
The ROTS versions stand out here as well
Luke Skywalker
I don't know that I have a favorite Luke but I bet the Vintage ROTJ one will have great articulation. I did like the X-Wing Luke that came packaged with Mara several years ago as well.
Princess Leia Organa
Vintage Hoth Leia
Han Solo
I love the articulation on the one that came packaged with the Falcon, but I'd bet the Vintage one will be just as good if not better.
C-3PO
There have been a few I liked a lot. The Episode 2 one with the interchangable heads was fun, but I seem to recall an ESB version from not that long ago that was great as well.
Obi-Wan Kenobi
ROTS, though I'm not much of an Obi fan.
General Grievous
The last Build a Droid, Legacy Collection one was said to be awesome. It's been a while since he was released though.
Count Dooku
For articualtion the ROTS one is great but I still love the bad ass Episode 2 version thats posed spraying lightning.
Commander Cody
Meh, no idea
Ahsoka Tano
We haven't seen enough Ahsoka figures yet to really get a good one. So far I'd say they are on the weak side.
Aayla Secura
Same deal as Dooku. The Episode 3 version is very articulate but I still like the more posed Episode 2 one myself.
Shaak Ti
See Dooku and Aayla
Asajj Ventress
I don't have a lot of Asajj figures, but of what I do have I like the 2D Clone Wars Micro Series figure just to be difficult
Luminara Unduli
See Dooku
Jacen Solo
The one Jacen Solo figure that been produced is awesome but quite rare.
Jaina Solo
The one Jaina we've gotten I don't like that much but beggers can't be choosers
Lando Calrissian
Just after ROTS they did a Cloud City version of him that is awesome with a cloth cape.
Padme Amidala
My favorite Padme is the Episode 2 Droid Conveyer belt one.
I have some of these figures loose that you can take a look at Scrapper, maybe at C4.