Indiana Jones and the Temple of the Four Hour Queue in DL is fantastic. Honestly though, the queues are what really separate the Disney parks from most other parks. Picking a favourite, in my opinion, is pretty tough.
The Fantasyland queues in WDW are a pale shadow of those in DL, so it's tough to point out any one in WDW.
Star Tours is amazing with the StarSpeeder and da droids. Tower of Terror really gets the mood going, especially if the misters are on in the garden. TTBAB is also excellent for the mood - the posters rock. Kali is very authentic (haven't seen E:E yet). And Great Movie Ride...I mean, the main body of the queue is a theatre, with the zig-zag replacing the seats - how more mood-setting can you get?
Muppetvision 3D, easily, hands down, is the best pre-show. I still lose it every time Rizzo comes out as Mickey.
Don't forget World Showcase either. While not authentic, the mine queue for Oh Canada! is nice, and the singers in the American Adventure are a nice departure from the hustle and bustle of the parks.
For memories though, Splash is my favourite. While an already excellent queue, my friend and I unfortunately next in line when it went 101. So rather than get bummed, we managed to get the queue doing a wave all the way back to the end. And following that success, we got everybody doing a very long train of Row Your Boat. With a 101, we had to create our own magic for the next 15 minutes. And it worked...the young ladies standing above us, at one of the rock openings, asked us to wait for them after the ride, which of course, we did...making for a even better remainder of the day at MK.