I put Brembo rotors and Akebono Pro-Ceramic pads on my Gen3 and loved the set-up. I'm considering the same for my current 4Runner, but will probably just go with the pads as my rotors are in really good shape... I just don't like the feel of the pads that are on there now.
I've also heard that NAPA's Ultra-Premium rotors are top notch.
~Doozi