they have different connections internally and newer hardware. the 1.0 and 1.1 have "daughterboards" for the controllers while 1.2-1.6b do not. also, the earlier drives have a very crappy DVD drive. the video chips also changed as the versions progressed. my 1.5 boots up about 3 seconds faster than a 1.0-1.2.
the 1.0 and 1.1 use a different power supply connector and i think the ram is also slower. the differences arent huge, but there are definitely a few.