Hey, nice thread. Off the top of my head:
Fishing in OoT.
The little wooden-arcade game with
In Mario & Luigi.
Any game with a colosseum you can battle in (such as Tales of Symphonia)... if that can be considered a mini-game, anyway.
Lucky-Hit in Shenmue 2. (Okay it wasn't that great but Ryo attempting to advertise it to passer-bys was hilarious). Don't forget all the real retro games you could open up in Shenmue, too.
Gambling in the first Pokémon games at the casino, way back in the day. (I remember doing quite a bit of that, for some reason).
All the minigames you could unlock in Jet Force Gemini! (Been meaning to play that game again, actually)
The target practice games in the various Zeldas. Especially fond of the horseback archery one in OoT.
The battleship game in Wind Waker. (Yeah Battleship is kind of boring too, but the clerk in that shop makes it the best mini-game ever. SPLISH)