It would be really helpful if your Wiki had a page that collected all of the available commands (e.g. contents of /bin) and listed them with brief descriptions of their functions. Something like part 4 of the page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands
(Might reduce the number of forum questions you get too). There are other commands listed on that page but without brief descriptions, you're forced to do quite a lot of additional navigation to determine what each command might do or else scan the contents of /bin for something that sounds like it might apply and then check the help output. If you could just collect the descriptions from the individual wiki pages or from the help sections of the code itself that would be great.
There also seem to be a number of useful commands that aren't listed anywhere in the Wiki (mni152reg, fslregister, etc) so that a typical user has no idea they exist.
--Ruth