Wheel braking is the main one used. This is aided by the spoilers, devices on the wings that when active reduce their lift to virtually nothing, so the full weight of the plane is on the wheels.
Reverse thrust is for extra braking. I believe for a landing to be allowed though it must be possible WITHOUT the reverse thrust.
Most runway over-runs result from failure to activate the spoilers, meaning the wheel braking is ineffective. Aquaplaning on a wet runway also occurs.