I have both the 2004 and the 2006. I just started comparing them page by page. My idea is to go through them side by side (at least the non-organ system part, section II), adding new topics or mnemonics to my annotated 2004 as I find them in the 2006.
So far I'm only through the behavioral science section, but I have already found a few differences. The 2006 has been edited in a few places to change wording and/or remove lines of text under certain subtopics--usually only minor changes with little change in overall meaning. Although I did notice that the 2004 has more HY vignettes at the beginning of the behav sci section. Also, I have found 2 or 3 subtopics and/or mnemonics in the 2006 that were not in the 2004, and a variety of very slightly altered formatting changes.
Overall, the changes are minor so far, but I expect there to be more differences as I progress through the sections.... we'll see.