The best "bang for the buck" is bikesdirect.com. The downsides are:
1. You must assemble the bike yourself or take it to LBS ($50-100)
2. If you don't wrench on bikes, you have to pay someone to tune is ($25-40)
3. Warranty support is over email or phone and sometimes requires shipping them the faulty part back. I broke a seat post, but they just sent me a new one after I sent pics.
4. No brand name recognition (if you're worried about that sort of thing)
Now, the good part is that you'll save $500-1000 over a comparably equipped "big name" bike. The quality is the same, as evidenced by MTBR reviews, members, riders, etc. I actually like my $700 Cliff 29er better than any other hard tail I've ridden for under $1200. Assembly is easy, and takes under 2 hours and just a small tool kit: crescent wrench, screwdrivers, hex wrench set, t-32 torx wrench (for disc brakes). And if you learn to tune a derailler online, that's likely all that will need to be done out of the box.
For $2,000 you're going to get a nice bike from the likes of Trek/GF, Cannondale, Specialized, etc. BUT, with bikesdirect for that same amount of money you'll get components that only appear on bikes costing twice as much. For instance:
Specialized Stumpjumper Comp 29 (great bike!) - $1800:
Al alloy frame
Reba SL 29er Fork
Avid Elixir R CL hydro brakes
FD: Shimano SLX
RD: SRAM X-9
Shifters: SRAM X-7
Crankset: Shimano FC-M542, integrated BB
Wheels: DT Swiss rim, Spec/DT Swiss Front Hub, Shimano M525 SL Rear Hub
Stem/Bars/Post: Specialized
Motobecane FLY Team 29 - $1999
Titanium frame (< 24# total bike weight)
Reba Race w/ MotionControl, FloodGate, etc
Avid Elixir CR
FD: Shimano XTR
RD: Shimano XTR
Shifters: Shimano XTR
Crankset: FSA Afterburner MegaExo w/ FSA BB-7000 external BB
Wheelset: Vuelta XRP Team SL rims/hubs
Stem/Bars/Post: Ritchey Pro
OR, if you want to save some cash and get a similarly equipped bike to the Stumpy, check out the
Motobecane Fantom Pro 29 SL - $995:
Aluminum Frame (~27 lbs.)
Reba SL 29er fork
FD: Shimano Deore
RD: Shimano XTR
Shifters: Shimano XT
Brakes: Avid Elixir Hydro w/ 185mm front rotor
Crankset: Truvativ FireX w/ GXP external BB
Wheelset: Gravity Forumula hubs/ WTB LaserDisc rims
Stem/Bars/Post: Ritchey Comp Al
IMO, I'd rather spend $1k for the Fantom Pro and maybe another $700 on a killer tubeless wheelset with Hope hubs than $1800 on the Specy. That's just me though, to each their own.