Okay then. Desert island single issue list. Here goes (in no particular order):
Doom Patrol #34: The issue with Mallah and the Brain that my avatar came from. No single issue has ever entertained me so thoroughly. Just absolutely hilarious and perfect from beginning to end.
X-Statix #24: I haven't gotten around to reading X-Statix as a whole yet, but I've already reread this issue twice just because it is just hilarious. The fight between Mr. Sensitive and Iron Man is one of the funniest things in comics I've ever read. And the Allred art is amazing too.
Hawkeye #6: The Christmas/Kwanzaa/Hanukkah issue. It's got it all: hilarious dialogue, heartwarming moments, badass Clint, and some of my favorite Aja art. There are so many moments in that issue that I love.
Daredevil #1 (Waid, the first #1, not the rebooted #1): That great Paolo Rivera art, that battle with The Spot, and just great writing in general. But mainly I'm picking this issue because of the fantastic back-up story drawn by Marcos Martin where Matt and Foggy are walking through New York City. It's just so well done as a whole and I was really impressed.
Space Punisher #1: Because it makes me happy. Totally ridiculous elseworlds story with classy painted art. I can't help but keep a massive grin while reading it.
The Punisher #4 (from Welcome Back, Frank): I love Ennis and Dillon's collaborations in general, but this issue where Frank gets chased into a zoo has so many amazing moments. There isn't much that tops Frank punching a polar bear in the face.
Batman #666: Because I'm unoriginal and it's an incredible standalone issue of Batman. It has so much depth for it for a one-off issue set in the future. Morrison and Kubert create a whole new world full of life just for one 20-something page issue. There's also plenty of depth in the story. Especially when re-reading it after having read the whole of Morrison's Batman run, it's really interesting to try and figure out what's what.
...I think that's all I've got. I might be missing something, but I've racked my brain and stared at my bookshelf a while and that's what I've come up with.
Quite a few of my all-time favorite runs aren't represented by single issues on this list, because in those cases, I would have had to just pick a random issue that wouldn't mean much on its own. For most of my favorite runs, every issue is pretty much equally fantastic to me and they all work together, so even though the stories as a whole are my favorites, I couldn't really justify putting one issue from them on the list.
I pretty much only went with issues that I could really enjoy without the rest of the run. So pretty much all the issues are either some of my favorite standalone issues or just an issue that really stood out from the rest of the issues in the run.