Gary Fisher is worth checking out for sure.
I bought a X-caliber last season, its really nice. Fisher has been making 29ers for awhile and are the best, IMO, for the $2000 and below price range. They have a bike just over 1k and one just under 1k. Lifetime protection on frame too. If you want to spend 1k, get a hardtail. Otherwise you will be getting lesser components to keep the price in your range. 29ers have a smoother ride anyway. Best advice: ride the bikes, buy what feels right.
Enjoy your purchase!