I use layers several ways.  

First I use it to hold lots of takes and mute the ones I don't.  If you don't save 5 or 6 you know the client is going to say "do you have that one I recorded 4 times ago?  It was perfect now that I think of it"  :)  Or you are playing a part with an old un-predictable synth, sometimes what the band played 6 takes ago fits perfect with the 9th take.

Second, if you have a sound that you want to "layer" and not have a bunch of different automation or levels going on.  I end up using this on old non midi synths a lot.

I also like to use them to archive multiple takes, and still have quick access.  If I'm working on guitar sounds and I have recorded several takes, I like to have a track that is  archived nearby, I can then drag clips to it to quickly clean up the current track and save the old work.