This has happened before. The last time it happened if I remember correctly it was more than 3 hours. Recently this is happening more frequently. As far as I know if it's for only a small amount of time, then theymos might be doing something which caused this.
It was the same weird thing which caused a few hours of downtime 6-12 months ago, and I think it's what causes the few minutes of downtime people observe every few weeks. I've never been able to figure out what causes it. It looks like the network gets cut between the web server and the database for a while. It seems to always happen at around the same time, so I suppose it's probably some automated maintenance process messing something up, but I don't have anything running at this time, so I wonder if it's something in the web-host's networking infrastructure, or something like that. It's difficult to diagnose, since it happens rarely, and usually when I'm sleeping.
I'm planning on upgrading the main servers sometime in the next few months. (Just as part of standard maintenance: there will be no user-visible changes other than perhaps slightly improved speed.) Maybe that'll fix it just by virtue of moving things to different areas.
(The few minutes of downtime just now was due to me doing something, and is unrelated.)