Recently I read a question on a forum thread on mtbr.com that asked if you needed to be concerned about a different sizing protocol for 29"ers than you would for a 26"er. Interesting question. The short answer is: No, not really.
You still want to concern yourself with the obviously important measurements: top tube length and stand over height, but that's not the end of the story. It seems that there has been a trend towards designing hardtails with shorter seat tubes and severely sloping top tubes. This is for both 26" and 29" hard tails, but is most commonly found with 29"ers, it seems. Some would argue that it's because of the tire size itself, but the seat tubes on some 29"ers are just plain short. Shorter than they reall need to be. Take my 18" Inbred 29"er, for instance. I have plenty of standover and I have to run a 410mm Salsa post to accomodate my leg length. If you are a long legged/ short torso kind of guy, you know this is a problem.
The mass manufactured 29"ers tend to have this shorter seat tube to accomodate more different sized riders on the same frame size. The Raleigh XXIX is a perfect example of this. After the seat height/ top tube issues have been cleared, there is one last 29"er specific fit issue to deal with. Handle bar height.
Most complete 29" bicycles come out of the box with riser bars. It's the fashion du jour, but it's not a good thing on a 29"er. Get that thing offa there and put on one of the new crop of flat, highly swept bars like the Niner Flat Top or the Salsa 11 degree bar. They will mimic the hand posistion of a riser without the rise. You already are dealing with a certain amount of extra height in the front end of a 29"er and a riser bar will only make it higher, and probably way too high! (unless you like being the Wheelie King!) Pay close attention to the bar height from a past 26" ride and try to get in that ball park with a new 29"er. You'll get along with the handling much better that way!
Hopefully these basic tips will help you if you are considering getting a 29"er anytime soon!