I have used both and have to say that I prefer WMX to WME - but they both basically do the same thing. WMX is by the guy who did the original Weapon Mod Kits mod for Fallout 3 (Antistar.)
WMX also makes a few logical changes to weapons - like adding common equivalents of This Machine and That Gun to be found throughout the game, which is a very good change, I think.
I also use WMX because of the compatibility patch with Fallout 3 Weapon Restoration.