This is hard... can I really only pick just one?
I have to say the attraction I miss most is "Tarzan Rocks!" The music has personal meaning for our family, the production was crazy and alive, and we miss it every time we go to Animal Kingdom.
Runners up? At MK, it's Wishes. I thought that was the best fireworks show ever. At Epcot? Maelstrom/Norway film- and the entire Wonders of Life Pavilion, as well as "Food Rocks." At the Studios, I really miss The Great Movie Ride. I can't ride anything that goes around in circles, nor anything with big drops. Losing TGMR was huge.