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The lighter weight of the C5 Z06 along with suspension that has less brake dive, cooling ducts keep the brakes cooler as well..... these are just a couple of things, Im sure someone else could point out a couple others.
MVR 155 has it right ..... the Z06 is lighter, and all else being equal, a lighter car stops in a shorter distance than a heavy car. The Z06 rims and tires are lighter, generating less rotational inertia. The Z06 has tires with a larger "footprint" on the road as the tires are wider (stock fronts are 245 mm, Z06 are 265 mm, the stock rear are 275 mm, and the Z06 are 295 mm) and this allows the Z06 to "grip" the road better. Also a stock Z06 has the Goodyear Eagle F1 Supercar tires (non-runflat) versus the C5 with the Goodyear EMT tires ..... the Z06 tires grip the road better due to a different compound and tread design. Finally, the Z06 brake pads are formulated to produce more braking torque sooner than the C5 pads. The trade-off is the Z06 don't last as long, and generate more brake dust than the stock pads.
So in a single "panic stop" situation, the Z06 has a lot going for it .... then if you look at situations where you are requiring the car to do multiple stops (say 0 to 100 to 0 MPH several times in a row) the Z06 has the advantage of better brake cooling, and being a lighter car, generating less heat in the braking system on each stop. Also the Z06 pads are formulated to fade at a higher temperature than the C5 pads ...
So .... there's just a few reasons the Z06 stops better than the "stock" C5 ......