There's a bit too much to list here, so I'll give you the Bulbapedia links:
Pokemon Mystery Dungeon: Explorers of Sky
Pokemon Mystery Dungeon: Explorers of Time and Explorers of Darkness
Since Explorer's of Sky is the later version, look under New Features to see what's different from Explorer's of Time/ Darkness (which are sister versions). There are a lot of small differences as well, with NPC changes etc., that don't really affect the main game play. There are a few new starting Pokemon/ playable characters added, so now you can be a Riolu etc. EDIT: Riolu was added in Explorers of Sky
I enjoyed the Explorer's of Darkness storyline a bit more, but that was just me. The Secret Bazaar feature in Explorers of Sky was pretty neat though; it made dungeons easier.