There are so many for me, I'll try to limit it. (If I could ONLY pick one, it would be Fantasyland in the MK)
MAGIC KINGDOM
I could say nearly everything in the park, but here are a few favorites.
* Everything in Fantasyland, especially at night! - The attractions are all favorites, and I love just being in the area an listening to the music loops, ESPECIALLY AT NIGHT! I enjoy watching the fireworks in Fantasyland, and riding the attractions in that section, especially after dark. I'm a big fan of all the characters and films on which the attractions are based, so Fantasyland is like a magical storybook wonderland for me. ALL 8 attractions in this section are favorites! Eating at Pinocchio Village Haus is my favorite spot to eat. I enjoy watching the It's A Small World boats go by, and also sitting on the outdoor balcony which provides a great view of Fantasyland.
* Riding Dumbo during the fireworks
* Toontown Fair - I love the charm of this section, the walk-through houses, the music loops featuring music from the classic Silly Symphonies and "Fab 5" animated shorts from the 20's and 30's, and riding the Barnstormer
* Main Street Electrical Parade - seeing this is a real treat, especially after not seeing it for so long! I like to see it at the beginning of the route, walk through Emporium/Adventureland, and see it again in Frontierland! The 11 PM parade is especially a treat, as it is less crowded, usually significantly so!
* Riding the front seat of Big Thunder and Barnstormer at night, and the front seat of Space Mountain anytime (since every ride is a night ride on SM!)
* Viewing my beloved Country Bear Jamboree, and visiting my "Laughing Place", Splash Mountain!
* Riding the Horse-drawn Trolley, the Railroad, and the Riverboat
* Visiting the Carousel Of Progress, and riding the TTA (especially at night, as Tomorrowland is beautiful after the dark)
* Doing the Adventureland attractions after dark with absolutely no lines!
* Eating an ice cream from the lower tables overlooking the Castle at night after the park is "officially" closed, but far from empty
* The lights on Main Street after dark, and watching them slowly fade away while leaving on the ferryboat (which is especially poignant on my last night each year)
EPCOT
* Spending time with Figment! And then going to see Quark the Dog in HISTA!
* Riding the Nemo ride and then spending lots of time with the fish, dolphins, and ESPECIALLY the manatees in the animal exhibit areas
* The dinosaur segment of Universe Of Energy
* Front seat rides on Test Track, at night
* The top row of Soarin' and the animal AA's in Living With the Land
* Riding Gran Fiesta Tour and Maelstrom in World Showcase
* The sublime perfection that is Impressions de France
* Strolling around the World Showcase lagoon at night, after Illuminations, and enjoying the music loops and architecture of the countries, which at this time are quiet and fairly empty (due to people still dining, in my experience, this area doesn't begin being "swept" by security until around 10 PM, if not later). And I agree about the garden area in Japan being especially beautiful after dark.
DISNEY'S HOLLYWOOD STUDIOS
* Fantasmic! - especially on nights when they do a 2nd show and I can do attractions up until showtime and walk in right before the show starts without worrying about it filling up!
* Walt Disney: One Man's Dream - I could easily spend one or two hours in here regardless of how many times I've seen it!
* Laughing at Mushu's antics in the Magic of Disney Animation attraction, and then enjoying the display previewing whatever Disney or Pixar animated film is coming next
* Watching the Beauty and the Beast and Little Mermaid shows
* The Wizard Of Oz finale of The Great Movie Ride
* Star Tours, including watching the humorous banter between R2-D2 and C-3PO in the queue area
* Riding the front row of Rock and RollerCoaster, and experiencing the sweet airtime of Tower of Terror
ANIMAL KINGDOM
* One of my favorite things to do in this park is to slow down and "talk to the animals"! I spend a lot of time just enjoying the animal exhibits throughout the park - Oasis, Discovery Island Trails, Pangani Forest Trail, Maharajah Jungle Trek, and Rafiki's Planet Watch. I love animals and AK is quickly becoming my second favorite park after MK, or at the very least has equalled Epcot for the second spot!
* Affection Section is one of my favorite places in all of WDW. I could easily spend at least an hour petting and visiting with the goats, sheep, cow, donkeys, piggies, and llama. The Dexter cow, named "Miss Kitty", is my favorite!
* Riding the Safari and enjoying the animals. This attraction is extremely well done, the best of its kind I've ever experienced!
* Enjoying the talented birdies in Flights Of Wonder. My favorite is Groucho, who can sing 7 different songs!
* Enjoying the sublime beauty of the Tree Of Life and spotting animals on the trunk, especially from the trail that passes extremely close to the Tree.
* Enjoying It's Tough To Be A Bug, another cute and heartwarming favorite!
* Enjoying the festive and fun Mickey's Jammin' Jungle Parade!
* Riding the front row of Everest, especially after dark!
* This park is beautiful at night. The Tree Of Life looks beautiful after dark. I also enjoy sitting in the Flame Tree Barbecue dining area at night, overlooking the water and looking at the moon and Everest reflecting in the water while listening to the Discovery Island music loop playing in the background. (My favorite tracks on this music loop can be heard in their entirety at the following link. They are tracks 6 and 9, and 6 is my favorite:
http://www.ufomusic.com/product.php?id=140 )