I have an 01 SXR500 I picked up last year. It is as close to showroom condition as you can get used. I picked it up to get back into the sport after a couple years out. Only put a few hundred miles on it last year and it's still under 2000 miles. It seems very reliable and if that is all you are after it is a safe bet. Contrary to what most folks say I found that the rear suspension went over bumps well, the front suspension was not as good.
it also darts around a lot, going to see if I can find double carbides for it this year.
Where I found the difference was when I got on a Polaris 6, and 700 last year when riding with a large group. I found each of the Polaris handled much better than my Yamaha, it left me a little dissapointed. On the Polaris they seemd wider, more stable, and definately did not dart like mine. As you can imagine the 6, and 700's where a bit faster, but that is not apples to apples. The yamaha 500 I have has OK bottom end,
(not going to beat anyone off the line) Top end actually surprised me a little, it's pretty fast on top. I hear you on the CAT macines, every single person I know who has a newer one has had some sort of problem(s). Lot's of clutches being rebuilt on or before 1000 miles, I have gotten thousands of miles out of my Polaris, and Ski-doo clutches in the mid to late 90's vintage. Arctice cat has a nice front suspension, and some really cool sleds, however they are notorious for problems.
Having said that I would probably buy a Cat F6 or 7 for the right price. Call me crazy..