The only place so far that I have found the diaper flannel is at Walmart. The thing that I noticed is that not only is it not as wide, but to me it seems like its heavier. possible woven tighter then the regular flannel. Both seem to work just fine though!
Diaper flannel is narrower, woven more tightly and generally only available in white. It is also double napped (brushed on both sides) for greater absorbency. Cheap flannel is sometimes only single napped, and you can see the criss cross woven fibers when you look at the surface. It will pill up after only a couple washes as the loose fibers twist around each other. Better quality flannel will have enough weight and bulk to it that the surface appears uniformly fluffy and it will last longer. Quilter's flannel is thicker, softer, comes in colors/prints and doesn't pill nearly as much. It is about twice the price of standard flannel, but worth it, IMHO.
The store I was at last night had all their flannels on sale for $3-4/m (including nice thick flannels. The quality isn't quite up there with the quilting store where it's usually about $10/m but it's less than a 1/3 the price and you get what you pay for...) The diaper flannel though was not on sale so for way less fabric I would have had to pay 2.75/m for considerably less flannel (and the fabric wasn't any better than the other flannel. It certainly wasn't much thicker) If you're cutting it out anyway, I don't think there's much point in using diaper flannel unless you get a REALLY good price on it.
I agree with the PP go for the quilters flannel or use an extra layer of the fluffiest cheaper flannel you can find. I've used the heavyweight flannel that wazoodle sells and have been very happy with it (and it's cheap and they ship fast if you purchase with a CC. It's pretty slow if you are using paypal.)