MK:
Big Thunder Mountain Railroad, Splash Mountain, Space Mountain, Buzz Lightyear's Space Ranger Spin, Peter Pan's Flight (why, I don't know). Pirates of the Caribbean usually has a short wait. Jungle Cruise gets longer late morning/early afternoon (we found early evening a good time to go). Carousel of Progress and TTA never have a wait (or, if so, it's 5 minutes or less). The shows (Mickey's Philharmagic, Enchanted Tiki Room, Monster's Inc. Laugh Floor) have lines that swallow up crowds easily due to larger seating space (especially Philharmagic). Hall of Presidents is rarely crowded as well. Haunted Mansion isn't bad early morning (10:00 ish). Whinnie the Pooh gets crowded as Fantasyland gets crowded. Wishes is a must. (Top of the Main Street Train Station had nice views)
Epcot:
Soarin', Test Track. Turtle Talk with Crush is a popular one, so try to get there early. Living With the Land generally has a 10-20 minute wait. Figment has no wait (or, if so, 5 minutes or less). Honey, I Shrunk the Audience is a semi-popular one, but again, as it's a show, crowds swallow up easily. Universe of Energy isn't too popular. Mission: SPACE is dependant on weather you do the Green or Orange side (less intense vs. intense). Spaceship Earth is a continueously moving attraction, lines move fast. Same goes for The Seas with Nemo and Friends (ride). Malestrom (Norway) is usually 5-30 minute range. Grand Fiesta Tour (Mexico) is 5-10 minutes (usually less). Illuminations: Reflections of Earth is a must. We tend to try and aim for the Cantina de San Angel (Mexico). It's right on the lagoon, and you can eat while watching (counter service).
MGM (DHS):
Tower of Terror, Rock 'n' RollerCoaster, Toy Story Mania! GET TO TOY STORY MANIA! FIRST!!!! THIS IS IMPORTANT!!! Lines are crazy-long, with even 30-minute waits for FASTPASS! MGM is mostly shows, so plan your schedule around what your kids want to see. MuppetVision 3D is the only show that runs on a loop, no set times (so go anytime). Great Movie Ride tends to have long lines (30 minutes general). Fantasmic! is a must (tip: if there are 2 shows that night, the later one is less crowded generally).
AK:
Expedition: Everest, Kilmanjaro Safari, Dinosaur. Kali River Rapids depends on the season (summer the line will be longer, winter the line will be shorter). Festival of the Lion King is a VERY popular show (and a must-see at that!). Finding Nemo: The Musical is also very good (we were indeed able to fit both 30+ minute shows in one day). The good thing about AK is that it's mostly walking and shows, not too many rides. (Primeval Whirl and Triceratop Spin are the other two rides, generally not too long of a wait for either)