I've been driving for about 30 years now, both manual and automatic. I've never had an automatic transmission problem, but I have had a manual go out on me. Mustang with a T5. Go figure. Never had a clutch go out either. Generally, manuals are thought to go longer, but add in the clutch... I think manuals have the edge, but there is no clear winner.
I think you also have to factor in the maintenance, and the actual transmission itself. For example, a lot of minivans seem to have transmission problems....not that I have ever had one, but I hear the distress stories about it all the time. Like, just a week ago my sister had her Pontiac Montana transmission with 70K miles go out, right before traveling for Thanksgiving and with Christmas coming.