The Nerd Herder, also known as The Herder, is the name given to the cars that belong to the Buy More's Nerd Herd, which Chuck uses both for his job at the Buy More and occasionally for his work with Sarah and Casey.
A standard Buy More Herder includes all-wheel drive, MP3 capability, and GPS navigation. It's painted in the red-and-white "Nerd Herd" color scheme, rather than the basic Buy More green and yellow. However Chuck's car has been heavily modified by the CIA. Later in the first season, the Herder becomes a Toyota Matrix.
The first of these modifications appears in "Chuck Versus the Helicopter". The Herder is known to have the following modifications: access to a GPS/tracking network, an ejector seat and passenger-side control system, an internal detention mode, the ability to be driven by remote control, a self-destruct mode, and a camera in the back seat.
In Chuck vs. the Sandworm, it is revealed that Chuck's Herder has been fitted with a self-destruct system, an auxiliary set of controls for the passenger, and an ejection seat for the driver. The car is also designed with a "Detention mode" which is activated via key remote, cuffing the driver in place and keeping them detained until further notice.
It was destroyed with a bomb by Chuck in the episode "Chuck Versus the Best Friend", when he used the remote control system to take the explosive device to a safe distance before it detonated. Chuck was not seen driving a Nerd Herd car again until "Chuck Versus the Colonel" and the episode did not reveal if this car possessed any of the same modifications as the original Herder.
Since Chuck and Casey manage to destroy the Herders on a fairly regular basis, the CIA presumably has several of the cars already modified that they can use to replace the current model without drawing Big Mike's attention.
The Herder and its extensive high-tech modifications are a less-than-glamorous nod to the modified cars featured in the James Bond films.