When you catch a certian number of banana fairies, you will get bonuses in the mystery mode option on the main menu.

2 fairys= DK theater; watch the cinematic sequences all over again.
6 fairys= Bonus levels
10 fairies= Battle the Bosses
15 fairys= Activate a bonus character in kong battle
20 fairys= Cheat menu, unlimited crystal coconuts, homing ammo, and banana coins.
Remember to go see the fairy queen when you rescue them all for another surprise.