I bought my refurb 2008 Mac Pro in mid 2008. Absolutely no issues with it. No scuffs, dings, dents, looks practically brand new. In other words, if you looked at it in passing you couldn't tell it was a refurb. And it's still going strong. (The refurb Cinema Display I got with it is another story...)
You get the same warranty as a new Mac Pro, and you can also extend it with AppleCare.
One thing you may need to consider is that you can't get a refurb built-to-order.
Also, all of the above only applies if you get the refurb machine from Apple directly, not from some 3rd party that may be selling refurbished Mac Pro's.