In order to force an
fsck check on reboot simply stick a file in the root of the filesystem you wish checked named forcefsck and reboot. You can use the line
touch /forcefsck to create it. If you have the filesystem mounted under another path edit the line accordingly. fsck will automatically remove this file when it is done with it.
If you wish to check a filesystem you can not mount for whatever reason boot into a live-CD (such as Ubuntu) and run
fsck /dev/sdXY where X and Y are your device and partition. Assuming the issue is not with your partition table you can use
fdisk -l /dev/sdX to help figure out which partition is which.
These commands may require root privileges depending on your distribution.