CanAm, we always do an auto draft, same as baseball. The reason being we are spread out time zone wise so much that an online draft would be really difficult. I play in another league in which we make our own picks online, and you're right, it is fun.
I also play a 3rd totally seperate league through work, and is very different. It's a salary cap league through espn, called Gridiron Challenge. This one runs in a completely different way also, no draft required at all.
The best thing to do is read up on the players, rank them to the best of your ability (or not, if you choose) and hope for the best. It's always a fun surprise to me.