GRAAAH!
So this was an unrelated problem to the other one, but has ended up being more annoying.
Some game was taking an infinite amount of time to host. That's a dom3 bug, not a llamaserver bug. While waiting for the game to finish hosting the server can't do anything else, which is why it appeared to have stopped working.
Well unfortunately, that meant I had to log in and prod it again. The llamaserver really doesn't do well with me prodding it, because it does things and I do things in parallel and bad things happen. The bad thing that happened this time was that somehow all the maps got deleted. That's pretty bad - that set of maps aren't stored together anywhere else. And I didn't back them up.

STUPID LLAMA. For some reason I backed up the mods, and the code, but not the maps.
Anyway, this has no effect at all on games currently running, but will mean that any new game that attempts to start will disappear. I've therefore put up a notice on the front page of the llamaserver to say that people should avoid starting games until I've restored the maps. I can restore any individual map on demand quite quickly though, so it shouldn't really cause problems.
I think what I will do is make a new page "Old Map and Mod browser" showing all the old maps which existed, and then start again with the llamaserver map list, with just a small set of maps. If you want to use any map from the old list which isn't on the new list, you'll just need to upload it again.
Man, how annoying.