There are quiet a few methods, none of which are available out of the box, except of course for any plugins etc.
You could take a look at : http://www.hi-voltage.com.au/codex.php
Ive used this in the past and it suited my solution at the time.
or http://www.installfactory.com/downloads.html - which has a filemaker plugin to complement security
or http://www.microcosm.co.uk - who have a filemaker plugin also
You could also integrate your own methods, however this really depends on what your solution is.
How secure you need it to be (i.e is it a $10 solution or a $10,000 solution)
Also, it is imperative that you remove 'admin accounts' when binding the runtime, otherwise your passwords can be recovered and anything you do can be bypassed by opening the files in Filemaker Pro