Hey Peter -
I just got my FZ about 1 month ago, so take my advice for what it's worth... Anyway, I picked up a 2006 model with about 3,400 miles on it. It is an AWESOME bike. It will cruise along nicely on your morning commute, or it will fly down the highway like it was shot out of a cannon. It is equally happy performing either task.
The only strange thing that I have noticed on this bike is the very small friction zone on the clutch. I thought for sure that I bought a bike with a toasted clutch - nope, that is just the way the FZ6 is... Also, some people do not like the stock seat and windshield. Mine is all stock so far, but am thinking about getting a taller windshield for longer trips.
As for which model year you should get, from my reading on this forum I would recommend 2007 or newer models. The '04-'06 models are fine, but the 2007 and newer ones are better.
Get one, and get it soon! You will not regret it.
Rob