I replaced the Avid brakes which came with the Trek FX+. before replacing the brakes I replaced the brake pads with Kool Stop Salmon. They squeaked like crazy but did improve stopping in wet weather. I felt I could do better.
I replaced the Avid brakes with Shimano Deore XT brakes and Kool Stop Tectonic brake pads. The Tecktonic pads are broken in to 3 small pads. One pad is for control the other is for aggressive and the last pad is for transition force.
It has been incredible to see the difference. With the new brakes it feel like disc brakes. If I would have known that new brakes would make such a difference I would not have bought the bike without upgrading first.
http://bike.shimano.com/publish/cont..._mountain.html
http://www.koolstop.com/brakes/index.php