As I recall, it was somewhere in there that BDM started manufacturing their own frames. One way to tell the difference is the cable guides on the downtubes - in the earlier models, they used a chrome ring around the downtube - on the newer frames, the chrome ring is replaced by a two-pronged guide that is the same color as the frame itself. Functionally, I don't think there is any significant difference between the two different frames.
One of the biggest changes was in the rear struts that support the back fender. The earlier ones were polished billet aluminum, while the later ones are chrome plated. More important is the sissy bar mounting system. The later struts include a hole with a plug in it, which can be removed to insert a sissy bar. Earlier models required replacement of the whole strut system in order to mount the sissy bar - a project that could cost over $600, plus labor. Just look at the struts on each bike - they either have the holes or they don't.
Big Dog does not necessarily introduce all their changes at the break in model year - meaning, you may find some 2006 models with some of the newer features, and some without.
Most of the changes were pretty minor - I don't even recall any others at the moment. They had a very successful model going, so they pretty much stayed the course. You should see some really great deals on the 2006's by now - and even the 2007's, for that matter.