So, the joy all started Sunday, when we were the victim of a barrage of story spam. Someone decided it would be fun to run a script that dumps crap into the story queue faster than it could possibly be voted down. What this was supposed to prove is still unclear, since anyone could see that this was possible. As I mentioned in a comment, this is akin to breaking a car window to prove it's made of glass, and generally demonstrates the room-temperature (in centigrade) IQ of the perpetrator.
We blocked this hole several times, in different ways (finally being forced to deny all anonymous story posts), and collected a nice list of cracked machines that the attacks were coming from. We are in touch with the admins of those machines, and will eventually find the person or persons responsible and seek legal action for abuse of computer resources.
After a brief lull, the attacks returned, this time flooding the comment forms with data. Another highly worthwhile DOS that proved essentially nothing. This as well was blocked.
Finally, this morning came an ordinary DOS attack, which apparently consisted of very large POSTS being sent at a huge pace. Unfortunately, on upgrading the code to block these, some changes got in that had not been adequately tested, and caused mysql to basically slow to a crawl. So for the better part of today, we've searched for the offending code, and finally rolled back to a previous version, which appears to be working at last.
In the midst of all this somewhere the database got hopelessly corrupted due to repeated abuse and crashes, and we were also forced to reload the DB from backups, losing about a day's worth of input. This sucks a lot, and I apologize profusely to anyone who's submitted a story that got lost. Please resubmit-- you were not dropped on purpose! As for lost comments, there's little we can do but go forward from here.
As mentioned before, hurstdog, Inoshiro, and everyone on #kuro5hin (IRC kuro5hin.ircnetwork.net) have been an enormous help in this. They solved most of the problems themselves, in fact, so we all owe them our thanks. I'll try to keep you all updated as the situation warrants, and thank you for your patience.