Looks like two very similiar bikes to me. I'd go by fit. If both fit and feel the same and none has a clear advantage in looks (I am serious, both bikes are that close)...
...I'd go with the Trek. The Shimano (and Avids on the 2011) brakes as well as the Rockshoxs Tora fork are known to work. Trek usually stands by their Bontrager parts. Might be the same for Cannondale, but I don't know that. My friends riding Trek bikes had good luck with them.