Pazaak in SW:KOTOR was fun. Like TCG blackjack kind of. The semi-3d special stages in Sonic 3 and Sonic & Knuckles were fun. I used to play those a lot.
Super Mario RPG for the SNES had a some mini game that you could play on some kids handheld in the game. looked like this. I cant even remember the mechanics but it was a lot of fun.
There was the Tower of Hanoi puzzle at one point in Mass Effect. It's easy once you know it, but I hadn't played it before and it was probably the most fun I had in the entire game. To put it in perspective, though, I thought Mass Effect was pretty dull and only remained playable due to its variation in gameplay.
I think Gears of War's active reload is the most significant mini-game in recent years. A tiny risk/reward gamble added to a simple mechanic but it's perfectly done. Gets you lots of small but satisfying hits as you nail one reload after another in the thick of a firefight. I honestly don't even know if it really does give…