Im riding a 2012 Gary Fisher Mamba 29'er right now, and I absolutely love it. A few years ago him and Trek kinda sorta merged and he has his own line of Trek bikes. If you want to go with a 29'er the Trek/Fisher line is hard to beat, with their geometry you feel as if you are in the bike, where with Fuji and Giants I felt like I was on top of the bike. If you are looking to stay in your price range you can get a decent 26" hardtail when it goes to a 29'er you can tack on about another $300. Just make sure to stay away from the 'v" brakes and go to something with a disc, if you can go hydraulic disc thats even better. Your other big price area is on your front shock if you are going with a hard tail. The more high end stuff will be more durable, and have more travel.
My Mamba was a little less than a grand, and you can expect to add another $400-$500 extra in accessories if you are just starting out when you look into add bike racks, repair kits, camel backs etc. Check out your local shops, a lot of times they will have bikes that people trade in when they upgrade to a newer model, or just realized they dont ride that much and decide to sell it. Im not a big fan of ebay or craigslist for something like a bike because you have no idea how well it was maintained. A bike shop will usually service a used bike before they try to sell it.
Another idea is now every month or 2 Trek offers 0% financing for a year, That will help you step up into a better bike and not hurt as much. They are also pretty generous with how much they will give you on the credit limit. I know my credit is pretty good, but I wasnt expecting them to give me a $4500 limit when I was only looking for $1000-1200. The last thing is that if you do get a nice bike dont skimp on the carrier, there is a thread on here that talks about carriers. I know Im not going to trust my bike to a cheap harbor freight type carrier.
Fortis cadere, cedere non potest
Poison Spyder BFH w/ trail stinger, custom rear BFH, crusher flares, rocker knockers, evap skid, hood louver. Rock Krawler 2.5 Max Travel, Teraflex rear tire carrier, River Raider cowl snorkel,Warn VR 10,000 lbs winch, sPod, Rigid 50"SR.