I like how Emeralds are managed in Generations. In Adventure 1&2 you saw Sonic collecting them, but really didn't get a sense of having them in an inventory. You just had to mentally keep track of who had what and how many, and in the end it didn't matter since he was just given them all.
Heroes special stages were a great idea, but sucked, and once you got all the emeralds you unlocked the final stage BUT couldn't use them as you would in the classic games. So collect the emeralds = complete the game, but no Super Sonic in regular stages. Lame.
'06 followed the Adventure method where it happened within the narrative. Not too exciting, and defeated the original purpose of the emeralds.
Unleashed did a pretty cool job. You had all the emeralds from the get go, but had to place them in the temples to reawaken them. Completing a stage = unlocking a temple = getting an emerald. I liked this approach.
Colors was on the right track, but I hated how red rings = more multiplayer stages = emeralds. Red rings should have unlocked artwork (like in Generations) and multiplayer stages should have unlocked when you completed stages in the main game. Red rings were just an unnecessary extra step towards Super Sonic.
