To force a check on your next reboot (here for your root partition), simply:

touch /forcefsck

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To manually do this, here is how to do it for the first partition on sda, when you are using ext4:

fsck.ext4 -fn /dev/sda1

• -f forces the check, even if everything seems okay.
• -n is a "read only" check, where nothing is changed and every question is answered with "no".
• When using dmcrypt, you probably want to check something like /dev/mapper/lvm-root.

This does not work properly when doing this on mounted devices (i.e. while your system is up), even when using the -n switch.

Kudos to Kim.