For me it would have to be Yoda, Count Dooku, and Anakin Hanger Duel.
I found Yoda behind a bunch of pegwarmers. It was the only one in the store and I think it was overlooked because it was so hard to reach and get at.
Dooku was hard at first, but now some are surfacing. Same with Anakin HD. But overall Yoda was extremely hard to find, and you can't find him anywhere anymore. He was so awesome in AOTC that he just gets snapped up whenever he is on the shelf, because everybody has to have him.
Can't say the same about Battle Droids or 3PO, they aren't pegwarmers, they are pegfirepits, they will still be on the shelf when Episode III rolls around.