I still miss Zul'Gurub.
It's been gone from the game since Cataclysm, but I don't think a week has gone by since it's removal (and eventual replacement with the current five man) that I haven't wished it was still accessible somehow. There were plenty of fights I hated in there, like the bat boss with her bomb dropping trash, but it was one of the instances with a strong, self contained feel to it - it really felt like we were raiding a place, storming into a stronghold with large stretches of outdoors, bridges, open bodies of water (with monsters you could fish up) and consequences to bad decisions - it was generally a very bad idea to pull Hakkar without killing at least some of the other bosses.
We did a lot of weird, stumbling runs in there, with 20 exhausted raiders fresh out of an MC run trying to get a couple of epics to fill gaps in their gear, and I didn't always have fun in them. But I find myself missing the place, and all the other raids and dungeons that have been removed and updated over the years. Shadowfang Keep, the Deadmines, Zul'Aman, the original Scarlet Monastery dungeons, and soon Blackrock Spire will join the list. I don't mind that content gets updated, but sometimes, I wish there was a Caverns of Time for content that got updated to let us go zone back and see it the way it originally was.
So what about you? Do you miss anything like this, or are you always glad to see it get swept away?