I ride a Stumpjumper FSR 29 and after adjusting for sag, have not been bottoming it out. Then again, I don't jump off anything big (< 8") and just use it for floating over rocks and some very small drops.
The 29" feel, on the other hand, is pretty sweet. You certainly feel like you're rolling over things easier. I moved from a hardtail 26" to a FS 29" so it's tough for me to experience it, but I hear that the larger wheels dampen the terrain a little bit, too.