First three dungeons? Let me think...
1. Some sort of electricity/plant themed dungeon. Remember how Kalle Demos had those electric vines? Or how Jabu Jabu's Belly was filled with electric monsters? The main item could be some sort of flail, which would be a combination of the Grappling Hook and Ball and Chain.
2. A water dungeon, like some sort of underwater palace filled with fish-based monsters. (Undead fish anyone?) As for the dungeon item, I was thinking an electrified boomerang shaped like a fin.
3. Simply a sand palace, like the one from ALttP. Also like it, have a power glove as the main item, except it can also be used to punch stuff. Like boulders. (I kinda ran out of ideas at this point.)