As an alternative to what MountainX described, name the file
~/.xmodmaprc.  The first time that file is present at login the user
will be asked if they want to load the file.  There is an option to not
be asked again.  Check that, select the file to load, and from there on
out the ~/.xmodmaprc will be loaded at login for that user.

Pro:  this can be a per-user thing, not requiring screwing around with
global files.

Con: since the file isn't loaded until after you log in, this means that
during the login window the ctrl/capslock keys have not yet been
swapped.  This may be confusing depending on the users of the machine.

If using a version of gnome that doesn't automatically load the file,
you could probably achieve the same effect by creating a "~/.gnomerc"
that invokes "xmodmap ~/.xmodmaprc".  Actually that's what I did at
first, and then was pleasantly surprised when gnome recognized the file
and did the right thing.

This was behavior was verified on a system running Hardy Beta that is
completely up to date as I write this comment.

-- 
Caps lock LED changes state even when caps lock is mapped to ctrl
https://bugs.launchpad.net/bugs/173350
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