Personally, I would look at a "new" leftover 08 before I would consider the 06. I personally think that the changes made to the throttle and whatnot are significant. Truthfully at this point in the year, I would wait until the 2010 models comes out and would get a "leftover" 2009 and save a grand plus on it.
In the end, with either a 2008 or a 2009, you would have a new bike instead of a used one, it would have less miles on it -and- in a few years when you go to sell it, it would be worth more than the 2006.
I always seem to have questionable luck with used equipement. Some folks take care of their stuff, others dont. With bikes, everyone seem to do farkles - some do a lot of farkles. I have seen some real hack jobs where guys have added farkles. With a "leftover" new bike, you avoid all of that and get a new bike with less miles and still get a heafty discount from a current model bike..
Random thoughts..