With the new R3 Season 9 boxed set out in local stores already, here's a summary of which sets are different from their R1 counterparts:
Season 1: Broadcast Episodes only, different (simple) special features, Amaray-type packaging
Season 2: Broadcast Episodes only, different (simple) special features, Amaray-type packaging
Season 3: Broadcast Episodes only, different (simple) special features, Amaray-type packaging
Season 4: Extended Episodes, special features the same as R1, Digipack
Season 5: Extended Episodes, special features the same as R1, Digipack
Season 6: Extended Episodes, special features the same as R1, Amaray-type packaging
Season 7: Broadcast Episodes Only, special features similar to R1 but missing commentaries and trivia game , Amaray-type packaging
Season 8: Extended Episodes, special features the same as R1, Amaray-type packaging
Season 9: Extended Episodes, special features the same as R1 but missing the trivia game, Amaray-type packaging