OK, so I know of an alternate way to beat Bongo Bongo other than incapacitating both hands and shooting the moving eye. The method goes like this:
Equip the Ice Arrows (previously thought to be useless) and fire them at one of the hands, much like a Longshot or regular arrow. The Ice Arrow, however, freezes the hand. The other hand now tries to break the first hand out of the ice. Now, take the Lens of Truth and turn it on, then find the eye which became visible to the Lens when the hand got frozen. Shoot it with the Longshot (or Arrow), then, if you got a good angle (sometimes you wind up behind Bongo Bongo when you do this), stab him like normal. The eye doesn't even move towards you using this method.
Added by: Blue Pikachu , ID#125