Originally Posted by Spats
Plake: "29 inch" mountain bikes use 700c rims. (Yes, the nomenclature sucks.) There are many such rims which are intended for MTB use, but people will still sometimes use tandem or heavy CX rims. It mainly depends on how fat a tire you want to run.
CX tires are a lot narrower than true MTB tires, which are at least 1.9" and usually 2.1". There are a lot of 29" MTB tires out now (WTB, Bontrager, Schwalbe, and others make them), though the big online retailers tend not to stock 29" parts. The only trouble is that the biggest tire available now is a 2.3" Exiwolf, so if you're looking for fat freeride rubber you're SOL.
The "29 Inch Wheeled Bikes" forum on MTBR is very active and will probably answer a lot of your questions.