I am looking for a way to have my control key and caps-lock key switched when I am in the emacs window, but when I go to any other program such as Firefox I want to be able to use the normal control button for new windows, tabs and such.
Additional Information: I am using Ubuntu, but answers for all systems are good since someone else may want to know how to do it on their system.
Emacs never actually sees the CapsLock keycode (under X anyway), so you can't remap the key in Lisp. Take a look at this page for details:
http://www.emacswiki.org/emacs/MovingTheCtrlKey
On windows using Auto Hot Key you can achieve this with this piece of code put in default script:
#IfWinActive, emacs@
CapsLock::Control
#IfWinActive
Auto Hot Key is a very handy utility and it is also free software like in GPL.
For globally remapping keys there is xmodmap. xkeycaps is an interactive tool. You can put control on both keys.
Since you want to remap the keys only for Emacs (which I find somewhat ill-advised) you need to look inside Emacs for a solution. It should be possible, because you can rebind all keys, but it may be too tedious to swap all keys around if the modifiers cannot be swapped.
Personally I map CapsLock to Compose, to type all kinds of funny characters like ä, ß, å, þ, «, —, ...