The 2006 (and 2007) had a bad throttle lurch from off-to-on throttle transitions (like when you get on the throttle entering a corner). Pay particular attention to this; if it bothers you, and the bike doesn't have a power commander, plan to spend $300 for a PC3/PC5 to fix it.
Also, look for the upgraded cam chain tensioner; if the owner hasn't done that yet plan on spending ~$80 for that if you do it yourself (it's not hard, just a PITA to get to). Not sure what a shop would charge to do it ... 1-2 hours labor, ~$200?
Pay attention to how it shifts. It's not going to be as snickery smooth as a Honda or Kawasaki; expect a "thunk" going into first, and a "clack" into the higher gears. That's OK. What to look for is that it stays in 2nd gear when you accelerate hard; it doesn't pop out of gear (bent shifter forks) or disengage/re-engage (worn cogs). Although merely a handful of us have had issues with this, it is failrly expensive ( > $600 in parts) and difficult (pull and split the engine) to fix and best not to buy someone else's problem.
Nearly all other issues with these machines are simple and easy to fix, from threadlocking the luggage locks, replacing the crappy stock mirrors or finding a seat / windshield combo that works for you.
There's another list here with lots of folks who have > 100k miles on their bikes, most with the original engine (one guy with ~ 360k). Don't be afraid of miles if it has been taken care of and is priced accordingly.
