We only see it from time to time, 99% of the time we see one of our cast in a car... it's an official agency car. When they're on official business they drive agency cars, hence why the car always looks similar even though Tony might be driving in one scene and Ziva in another.
The last time I remember seeing it was Jack Knife... but that's because it was used a lot. I don't recall if we've seen a minor scene here or there.
Using these old cars on TV is tough: as cool as they might look they tend to be just "barely" running.
For example, Supernatural uses an old Imapalas and on TV they sound like a NASCAR racers. When it fact most of them barely run and those that run well sound like how you'd imagine an 30+ year old car would sound if owned by a regular Joe. All of those engine sounds you hear are just the FX guys adding it.
No idea what shape Gibbs' muscle car is really in... maybe it really is well tuned and restored... or maybe it's just an awesome shell on a beat up V6.