An .rel file lets you play a certain stage on a stage that it doesn't play on (you have to change it first).
Example, you want to play a Final Destination-based stage on another stage (let's use Battlefield). You change Final Destination's .rel to match Battlefield's, place it in pf\module, and rename it to st_battle.rel.
Here are a bunch of them I did:
http://www.mediafire.com/?sharekey=8d2d9e36d3a57ec890a82c7bb0fad7ad1f4fca4ba97e09c9b878de785cc0f59eHere's the wikia artical if you don't understand still:
http://ssbbcustom.wikia.com/wiki/Module_files