How much test riding have you done on each? The Synapse's geometry is a bit more laid back than the Madone's. I like my '07 Synapse, but I also bought it without too much idea of what I was doing. Is it the best bike for me? Probably not, but I really have no idea.

One thing not fit-related is that the Synapse frames are mass produced in Asia, while the rest of Cannondale's road frames were hand built in the US (at least through '08 - things do change I know). I don't know how Trek compares on that front or how you feel about all the many issues that that brings up, but it's something to think about.