Since all files are backed up to your server, you could try your Hardware Test disc (I think this till comes with OS X these days). See if the hard drive has gone bad. If so you might need to get a new one.
My guess, though, is the master directory for your drive is now bad and you're lucky you can see it or its contents. A reinstall from the install cd can replace your OS X without wiping your hard drive. (If you do a "wipe and install" this will remove all apps and settings and wipe all data from your hard drive and instally a fresh OS X, minus any updates available for it.)
The other thing you can try is to do a repair while booted in single user mode:
reboot while holding command + s; hold keys till black screen with white text appears/type fsck -f/type reboot when finished. Hopefully this gets your directory back in order.
You might need to wipe and install to fix this issue, but try this Single User Mode first.