On the DCClassics.Com
checklist, a superscript "1" denotes if a figure was rereleased in WGSH/All-Star packaging. For the most part these are the exact same figure being released. I can only think of two notable exceptions. The latest Superman release (there's no way to tell via the packaging) had a brighter slightly different shade of blue and sharper eyes than previous versions - he's the same as the one released in the Parasite 2pk. The other exception is the last Flash reissue where they used the incorrect buck which gave him the larger, more-muscled torso instead of the basic body.
BigBot is correct about the TRU exclusive All-Stars though. I kinda considered those a separate SKU than the normal ones, but those would be four different versions of those characters.
This article details all the Batman releases through 2/2010: http://www.itsalltrue.net/?p=4005
Since then, there's only been the Sinestro Corps, Modern Age, and Golden Age Bats.
As for Superman, he hasn't had the minor difference releases like Batman. He's available in alternate costumes like Electric, Electric-Red, Mullet, and his Regeneration suit. There is a regular version with red eyes, but all other releases are basically the same minus minor changes in shade due to production issues.