Yes, there are several systems.
The simplest are REALLY BIG WINDOWS (and binoculars):
When the entire wall in front of you is a big expanse of glass looking out over the runway there's a good chance you'll notice something trying to roll onto the runway.
Many runway incursions are detected visually.
Really big windows don't work as well when you have multiple runways and larger airport complexes though, so we have some technological solutions too. The most common is Automated Surface Detection Equipment (ASDE), the one being deployed today is ASDE-X.
This is basically "radar on the ground" which interrogates aircraft transponders and shows the controllers which aircraft are where on the airport surface:
There are also systems on the ground designed to prevent incursions, but those are mainly for use by pilots.
These include Runway Status Lights, taxiway guidance lights (which include "stop bars" that light up on hold-short lines), and "runway guard lights" (which may be mounted either in the pavement or alongside the taxiway/runway intersection).
Many of these systems can be controlled from the tower, either by automatic systems or manually by the controllers.