When I repainted my wheels a few weeks back I noticed that my brake rotors were really shot. I was also getting some noise from the rusty bits of the rotor rubbing on stuff which really annoys me. I checked the pads and they still had ~1/4" left on them so I left them alone. Anyway, its pretty straighforward, but here is how to replace the rotors. Now would also be a perfect time to inspect the pads and replace them if necessary too.
First, we jack up the car. Make sure to use jack stands!
This is how my rotors looked. As you can see, there isn't a lot of brake surface area left on them. They still stopped alright, but its not a pretty sight and if I needed to stop in an emergency it might have been a problem.
Now, remove the two screws that are in the rotor. It is handy to have a manual impact driver to do this. A bit of heat from a torch might also be enough.
Next, we'll remove the caliper. The bolts are on the back side of the rotor.
Once the caliper is free, use a wire to hang it so it doesn't hang by the rubber hose.
Now, the rotor is free to come off, or at least it should be. Mine was rusted on a bit. It took some penetrating oil and a small sledge hammer to the back side of it to pop it off.
To prevent this from happening with the new rotors, put some anti-sieze on the plate the rotor mounts to.
Now, grab your new rotors, and clean the oil off of them with brake cleaner (carb cleaner and other solvents work fine too). After cleaning them, try not to touch the surfaces that the brake pads touch. You don't want oil/grease/anti-sieze in your brake pads.
Next, put the cleaned rotors on the mounting plate and reinstall the two screws.
Now, put the calipers back on.
Lastly, put your wheel back on, drop the car, and torque down the lug nuts.