I'm in the process of overhauling my trusty commuter but I seem to be having a right royal faff-on sorting out the brakes.
Stock brakes are Tektro CR720s on the front http://www.tektro.com/_english/01_products/01_prodetail.php?pid=5&sortname=Brake&sort=1&fid=2
and Tektro Oryx's on the rear http://www.tektro.com/_english/01_products/01_prodetail.php?pid=51&sortname=Brake&sort=1&fid=2
Not sure why Specialized didn't stick the CR720s on the rear as well but I presume its something to do with cable routing.
I purchased some Tektro Mini-V brakes to replace them as I've never been too keen on the stopping power and a near-crash into the back of a car in the wet a few months back sealed the need for new stoppers. I've had problems with them working with the Shimano STI brake levers as I have interrupter brakes on as well and they don't seem to play nicely. I've heard you can get something called a 'travel adjuster' but these are costly and to be fair I could buy a decent set of replacement cantis for the price of two of them.
Unfortunately disc brakes are not an option as neither frame nor fork has the required fittings.
It would be interesting to hear what people on here are running on their bikes as the Tricross seems to be a really popular bike