Some folks run the slip yoke at the bottom of the shaft, I know I always have. But also it could be a little hard on the shaft/u-joints banging around under the truck when hitting bumps, at least on a long/high speed trip:
http://board.marlincrawler.com/index.php?topic=38294.0;highlight=flat+tow+driveshaft

I know Marlin recommends disconnecting the rear drive shaft for flat towing. Problem is there is no true neutral in the t-case (unless you have twin sticks), so you either end up spinning most of the t-case parts in 2H or in 4N. And supposedly one of the bearings inside is not too happy with that.

Of course if you have a rear driveline disconnect or a full floating rear axle w/ locking hubs, you would not have to.