Hi Duck. Sorry for the rude hello.
Those are both nice makes, as you probably already know. What Cannondale are you looking at? An R2000? I'm assuming you've got it down to a pair of models that offer comparable component specs (like the Ultegra drivetrain); beyond that, between the R2000 and the Giant TCR1 Composite, it's going to come down to personal preference and fit.
I believe Giants are made overseas, unlike Cannondales, which may or may not be an issue to you; their workmanship is excellent though.
One significant component difference, presuming we're talking about '04 models (it may also be the case for the '03s), is in wheelset choice: Cannondale specs the R2000 with Ksyrium SLs while Giant specs the TCR1 Comp with cheaper and heavier Ksyrium Elites; figure that into your price/value determination.
The advertised perk of the Giant is, of course, the frame material; the sell is going to be a light, snappy and low-vibration ride. That may seal the deal for you... but you won't know until you test them out. Aluminum tends to be harsher, but modern higher-end alu frames can be quite comfy. Not everyone prefers carbon over aluminum.
So get out there and ride them! Good luck, have fun.