The one I miss most is the Adventureland Veranda. I did the "get your picture taken with Captain Jack Sparrow" thing last year so I could walk through the old restaurant.
Also miss:
Akershus the way it used to be, with the hot and cold buffet boards and Norwegian food.
Tusker House and Kusafari Bakery at the AK for a nice counter service.
King Steffan's at the castle.
Plain and Simple (I think that was the name, it was at Wonders of Life) - I remember getting a good fruit smoothie there once before it closed.
(We also miss the chicken that came out of the clock and crowed at the old Sunshine Seasons! Even though the counter service there is still ok, it just doesn't seem the same without that chicken.)
Wish we would have tried:
Bonfamile's - its hard to imagine a whole resort without one table service restaurant!
Ariel's - we've walked by it and it looks just beautiful.
Empress Lilly - I thought it was neat that there was a restaurant named as a tribute to Mrs. Disney, but the new name has never appealed to me.
Crystal Palace - before it became a character buffet.
Wish was still open:
The Odyssey - that place always seemed to be packed! Future World could really use another counter service restaurant.
Pasta Piazza - again, Future World could use another counter service.
Plaza Pavillion - I've never been there when its open as Noodle Station.
El Pirate y el Perrico - open seasonally, but never the season I'm there! Sometimes I'd just like a taco when I'm in the MK.
The Catwalk Bar - I think that's what it was called... above the Brown Derby.
Wish it was like it used to be:
Fountainview - I liked it better with coffee and pastries!