The primary difference is the sights. The newer 92FS comes with a pretty nice set of white dot sights, while the M9 has slightly smaller, plain black sights.
Some M9's have metal guide rods, but all of the M9's I've dealt with in the Army have had plastic guide rods, same as the 92FS.
Pretty much the same pistol.
You didn't ask, but I'll throw this in as well: The M9A1/92A1? Light rail added at the front of the frame, and a change to the checkering on the grip.