I was playing with FUSE, and had managed to mount a loopback filesystem. And then, for some ill-considered reason, I tried to delete the directory that I had mounted it inside.
I managed to Ctrl-C it before it ate any files in /home, but I still had some nasty cleanup work to get the computer back in working order again. Thank god for LiveCDs.
In the same spirit, I once removed a chroot tree, forgetting I bind mounted /etc into it.
It took me half a day to recover from that.
Another one, even more stupid, is to recover a "backup" of /var, done without the proper rights to it. I noticed the problem after a lot of weirds errors cropping in. This one I did not recover - after a few hours, I ended up deciding that reinstalling linux on my machine would be faster and more reliable.
I managed to Ctrl-C it before it ate any files in /home, but I still had some nasty cleanup work to get the computer back in working order again. Thank god for LiveCDs.