Primary difference is that BTX has the board mounted on the other side of the case, BTX also modifies where many things on the board are located, obvious difference is the location of the memory slots being along the top of the board instead of the front
http://upload.wikimedia.org/wikipedia/commons/thumb/0/0d/BTXformFactor.JPG/800px-BTXformFactor.JPG
Edit: Damn it, im typing slow tonight
@twoboxer: that isnt always true, i have seen a few HPs where they mounted the board upside down and on the left side of the case so coming up from floor level its I/O Panel, Expansion slots, power supply, this puts the motherboard on the left but its still an ATX