Allow me to not answer your question fully.

Here's the things I like:
Trek: Deore RD with 32 tooth largest chainring in back = better climbing or just low geared "wuss" days.
Alloy fork = more utilitarian (In my opinion), which is a good thing.

Specialized: R-440 shifters are very nice (Tiagra quality at least).
Nimbus 28c Armadillo are just about perfect for commuting and general road riding. A good balance of speed and comfort/durabily.

So, if only you could combine the two...which would have led me to recommend the Fuji Absolute. A bike which does combine all of those, at a cheaper price tag. In fact, once upon a time I bought that bike, and eventually tired of the flat bars a spent a deal of time and money converting to drops. (There's a lesson there.)

But then I went to Fuji's website, and saw that with the new 06 model they totally screwed them up, and it's not anything like the bike I had. They even added those crappy "motorcycle" style twist grip shifts. Not a fan anymore.

So now...man, that's a rough decision. I don't know what to say anymore, since my recommendation evaporated.

My $.02? The things I don't like about the Specialized the most are what's driving the cost up: The carbon fork and seat post. But...if you bought the Trek, and changed a couple of things if you wound up not liking them, would you eventually equal the Specialized price tag?

Perhaps...get the trek, and put those 28c Armadillos on for $50 extra dollars.

How was this for a non answer with lots of rambling?