My top excursions have to be, in no particular order...
Mayan Ruins at Xunantunich (Belize) - A really authentic, historical experience. I climbed half way up the tallest ruin there, and DH went all the way up. Climbing all the way up isn't for everyone, since the steps are pretty narrow.
Dolphin Encounter (Roatan) - The day we were in port, it was raining. Everybody's beach day was pretty much washed out...but we had a fantastic time with the dolphins. DH was rather skeptical at first...but he couldn't stop talking about it afterward!
River Tubing (Ocho Rios) - A little chilly when you first get in the water...but these guides are loads of fun, and the nature you see while floating down the river is really beautiful. There are some rapids, too...and they snap your photo from the shoreline while you pass by. A fun adventure.
Helicopter Tour (Kauai) - Lush, tropical island. Fantastic views. And from a helicopter. Can't miss it.