The current refurbished iPhone 3Gs available from AT&T and some Best Buy retail locations are NOT Apple Refurbished. They are refubished by a third party in the case of AT&T. If they were Apple refurbised they would come in different packaging and with a different serial number.
They come with whatever was on the iPhone 3G the first time it was sold. Some have been 2.2.1 others have been 2.2 and some have even been earlier in the cycle. The longer you wait the more likely that all future units will be 2.2.1 or later.
They all are covered by a 90 day or more Apple warranty. If you get a lemon, just take it to Apple and have it replace with a true Apple refurbished iPhone 3G. Most of the current units are from the holidays and have an original in service date from Oct 2008 - Feb. 2009.
Dave