How often should I do this? I had this server for 3 months now, serving big files. Also, if my server crashed.. will it run some sort of disk checking utility when it's rebooted or do I have to manually run a script to check the drive?
Depending on which Operating System you are using, if it is Windows, it is adviseable to do regular scandisk and defrag if you do a lot of file changes on the harddisk, once every few months would not be a bad idea. If it is for *nix then there is no Defrag that need to be done.
If a Windows server crash, it might activate scandisk during a reboot and on *nix, it would run fsck which is its equivalent. As to how long it takes to complete the scan would depend on how much files there is and how huge the harddisk is.
Also most *nix filesystems now in use are so-called journaled file systems (ext3, reiserfs, xfs) which maintain integrity of the filesystem in case of crash. Therefore all you could see in the log would be "hda1: recovering journal... done.". This message might land in dmesg, too.