Ride them all and see which one you like more. I ride a Marin Muirwoods 29er daily but I'm more about getting there comfortably on the beat up streets of SF. It's nice not having to constantly dodge every road imperfection and not having to worry if I accidentally hit a small hole in the street.
The bigger tires will soften the ride a lot compared to the flat bar road bikes I tried, but the Muirwoods definitely feels more sluggish. I didn't ride any Trek FX though, only tried some Scott and a Marin Highway One (I think).