Thanks caffeinewriter, any help is appreciated. I will file a report on Monday, and see what they say.
As for the cleaning up I think I'm OK. Just running clamscan over all the files, rkhunter had nothing to complain, but I don't know whether an eventual rootkit wouldn't be smart enough to fool them, any experience about that?
Let me put it this way. There is nothing more annoying than Rootkits. They hide in every dark corner of your system. I'd recommend a specific rootkit detector/remover. Here are some I know of.
If you still think you might have a rootkit, wipe your system clean. It's really the only surefire way to get rid of a rootkit.
I think after a disaster like this the only secure method is to reinstall all affected computers, make some images of the harddisk so you can still analyze what happend.