There are two things that stick out for me that aren't around anymore:
At Jiko a few years back, I had these amazing braised lamb shanks served over cous cous. I can't remember if they were a special or just a seasonal item, but I've been back a couple times since, and they haven't been on the menu in any form. I tend to order different things depending on my mood (I'm not the kind of person who sticks to the same order in favorite restaurants), but I would definitely order that again.
The other, I know was a regular menu item, and quite a popular one from what I understand, and that's the catfish and cheese grits at Coral Reef. That was an amazing dish. I was told last time I was there that the chef pulled it because he wasn't able to get the same quality catfish he used to, so he didn't want to put out a dish not up to his standards. I can respect that. I just hope that he finds some good catfish again someday. I'd love to have it again, and I can't make it nearly as perfect as they can.