I prefer the FE over the FM. The FE uses a needle in the finder for the meter, as opposed to the simple LED lights in the FM. Also, the FE uses interchangeable focusing screens.
Also, the FE has a greater shutter speed range if you use the automatic mode. If you are taking pictures of the stars at night, simple set the camera to A, and you will get a good exposure. Ken Rockwell says that the FE shutter will go as fast as 1/8000th in A, but I haven't tried to verify that.
I have the FE, FM, FM2, and FM3A, the FE is far and away the best value for the money.