Well, here's what I would do.
1) Turn off the computer for about a minute
2) Insert a boot disk and turn on the computer
3) Get some virus checker (hopefully on floppy) and scan your system thoroughly.
If you don't have a virus you should then run something like DiskSalv. I assume you're running the standard FFS? DiskSalv will give you a good idea of what's wrong and it might even fix everything for you. It's possible that you might lose some files and might need to re-install. Do you have backups?
How old is your HD? It might be getting flaky. Might wanna buy a new one. This reminds me, I should backup my A4000 soon.
- Mike