I have the Cannondale Cyclocross '05 as well. While I am generally impressed with the frame and fork, I also realize that the stock parts eventually have to go, in this case the wheels and the brakes. One thing to remember is that this bike is a cyclocross race bike, and is not really intended for triathalons or touring/commuting despite those silly and pointless rack eyelets on the dropouts.
As far as the brakes go, in a cyclocross setting they work fine, especially when braking on technical trail sections. The only drawback has been some squeling sounds from the brake pads against the Gipiemme rims when a new coating of mud or moisture gets onto the pads or the rims.
Remember, this is the very same frame and fork the Enrico Franzoi, the Italian national cyclocross champion and former U23 world cyclocross champion was racing on for a few seasons prior to Lampre switching from Cannondale to Willier. The only difference was in his component selection, which was mostly Campagnolo.