If you take the car out and don't park it back in the garage, it should end up at the impound if you are forced to use a different car for a mission, or if you get busted or wasted.
I've just been duplicating the cars in the garage so I don't have to worry about retrieving them from the impound.
Mod a car up however you like, then park it in the character's safehouse garage, walk away until the garage closes (or in trevor's case, walk out to the street) then save on foot from your phone. Immediately after saving, load up the save and you should have one copy of the car in your garage and one outside the garage. Now you don't have to worry about retrieving them from the impound or blowing them up.
This trick still works in 1.04.