This is something I'd like to do for 1.0, and also one of the reasons that I think the 1.0 name is useful. It's a non-backwards compatible change, but one that's small and useful. I'm leaning towards .ade for the parallel with Processing and .pde, but .ino is tempting too.
Its a simple text file, so whatever name you gave to it, it will always be possible to open the file usando the arduino ide, or any other editor.
PLEASE use a file extension longer than 3 characters.