I really like the Goron racing in Majora's Mask, the Flight Tower in Wind Waker (east of dragon roost I believe), and the rapids in Link's Awakening to name a few. There have been a lot of fun minigames in the history of Zelda, imo.
i'm a big person when it comes to the bow.
so I like almost all the shooting games.
however, the STAR game in TP was also fun once you figured out the second time around.
minigame? jeez...my favorite is probably TP fishing, and the STAR minigame.
Just as a bonus, my least favorite: the archery game in Phantom Hourglass. that game was HORRIBLE!