The Trek has Bontrager wheels.The Giant and Cannondale have Ksyriums.The Cannondale and Trek don't come with pedals.They'll all be close to the same price once I swap a few parts.Out of these bikes which would you pick and why?

Giant, for one, it's lighter. It might even be a little stiffer because of the compact geometry, but I've never ridden one so that's just a guess. Also, you can them for cheap, there's a guy who I see on Ebay all the time with a buy-it-now for 1049, that's frame,fork and headset. For me, that's the best deal, because I only use stock shifters and deraileurs. Every thing else is "custom". So that's my choice as far as the frame goes, I don't know much about any of the wheels.

I have the Giant Composite 0 and can say it's the best bike frame I've ever ridden both for lightness, stiffness and ride but I suspect you can't go wrong with any of these! Compact geometry isn't for everyone though so that could be an issue for you .. Have you test ridden any of them? I bought the frame from a guy off of eBay and that was the issue for him - his loss was my gain. You can find good deals on the composite 0 .. the one I bought had less then 500 miles and I paid $900 (frame, fork, headset). They retail around 1500.