Having recently purchased a 29'er and riding it exclusively for a few months (before getting ready for the 24 Hours of Moab) and now switching back and forth between it and my freshly rebuilt Cinco, I feel like I can give an educated opinion on this subject. I just made a similar comparison over on the Dirt Rag forum and a guy flipped out that I haven't whole heartedly swallowed the 29'er Kool-Aid. It isn't that I don't like a 29'er, it is just that I wouldn't use it personally in all applications. Let me explain...
I used my 29'er in Moab for the 24 HoM as I stated. It was a PERFECT bike for sand and the wide open course there. I think a 29'er shines in those open, non-technical (in a twisty, turny sense, not a rocky sense) type of rides/trails. Conversely, I think a 26" bike is easier to handle in tight, twisty singletrack. Here is a comparison.
I compared the two bikes in similar circumstances on my local singletrack. I have a loop that I do in the mornings before work (or at least when there isn't snow on the ground). Basically, it is a switchback climb to the summit then a long, swoopy, twisty descent back around the mountain. Nothing too rocky or technical. The 29'er climbed a bit faster but the 26" descended faster. I am able to "throw" the 26" into corners better than the 29. As Egordon said, the 29'er does have a gyroscopic effect, which to me makes switching the direction of the bike rapidly more difficult.
I guess the bottom line is try before you buy. Go to your LBS and see if you can rent one or take it out on some singletrack that you're familiar with. See if you like it. I like mine a lot, but as I said, it wouldn't be the only bike for me. But that is cool, cause you know the old saying "How many bikes do I need? Just one more...."