Definitely do all the shows if you can (there is always a list of times just thru the front gate). I took my parents who had not been since the early 90s and they were amazed at all the shows and how good they were. Dad said when leaving that he liked the shows best (and we thought he wouldnt!). They had much more fun than they did when we were kids and they had to worry about us getting lost or getting sick, etc. Its so fun going as/with adults!!
Animal Kingdom:
Festival of the Lion King show (amazingly wonderful!)
Finding Nemo: the Musical (ditto!)
Kilimanjaro Safari (it was lightly raining and kind of chilly when we went but we still saw tons of animals)
Tusker House for lunch was great (buffet)
Hollywood Studios:
Beauty and the Beast stage show
Little Mermaid show
The Great Movie Ride
Lights, Motors, Action (not my favorite, but my dad loved it!)
50s Prime Time Cafe (just for the atmosphere! very neat place!)
Backlot Tour
Indiana Jones
Osbourne Lights if during the holidays
Epcot:
Soarin'
Living with the Land
Spaceship Earth
Finding Nemo ride to the aquarium as well as the aquarium itself (if you like dolphins they do feedings and interact with them, I think its like 2:30 OR 3:30 not sure, they have a sign up though)
Coral Reef Restaurant (the wall in front of you is the aquarium!)
Walk thru World Showcase and do all the short movies, etc. Very neat!
Illuminations (just, wow!)
Mission Space
Test Track
Magic Kingdom:
Pirates of the Carribean
Haunted Mansion
Mickey's Philarmagic
Spectro Magic and Wishes
Crystal Palace lunch
Train ride (I never usually do this but my dad wanted to ride the train and he really thought it was neat)
Also ,if you have time, take the monorail and check out the resorts on it as well as take the boat to see the Wilderness Lodge. We would never pay the price to stay at a deluxe but its nice to go there and sit in the huge lobbies and enjoy it for a little while.
Also, dont forget downtown disney. And Wolfgang Puck Express (wish we could have eaten there more than once it was sooo very good! if there is a line, dont let it fool you as they usually have alot of cashiers and can move thru the ppl very fast)