I think it all depends on the trip. How long, terrain, passengers etc. You could get a basic trailer with a Thule type rack and a roof top tent and have the best of both worlds. You could run just the tent on the jeep, tent on the trailer for better highway mpg. Just use the trailer to haul dirt bikes, kayaks, etc.
A few other factors to consider:
According to some test by an Australian over landing magazine, a roof rack and roof top tent causes will cost you more gas than a trailer since the trailer is in the jeeps slip stream on the highway.
In some states, a trailer comes with a 55mph speed limit if you don't want a ticket.
I subscribe to the Scott Brady school of thought and want as little weight as possible on the roof. It's just safer.
Speaking of safety, roof top tents have another advantage. I've been reading this thread on ExPo:
http://expeditionportal.com/forum/showthread.php?t=10705
Most of these freaky stories would have been avoided by sleeping in a roof top tent, from lions and tigers and bears to Zodiac killer style murders. It would be quite difficult to shoot or stab an unsuspecting couple if you couldn't see them and had to climb a 7ft ladder to reach them.