Ok...
two things I really miss, and REALLY wonder about - the frogs and the bunnies at OKW and deer sightings almost every time riding the monorail to Epcot
*chicken satay at Tusker House before peanuts became an issue
*the fried banana caramel cheesecake egg roll at a little kiosk in AK
*water birds (specifically swans) and floating flowers in the water below the bridge when passing from Future World to World Showcase
*the orange smell in Horizons
*Club Lake Villas (is now SSR resort)
*merchandise variety - someone else mentioned the shops at the Disney Village, miss those so much, and also the stores in the earliest Pleasure Island days
*Crystal Palace before it became a character meal
*Restaurant Akershus buffet before it became a character meal
*breakfast at Trail's End
(Though I do really miss those things, there are certainly as many new things that I love!)