In Saints Row: The Third (aka Saints Row 3) for the PC, PS3, and Xbox 360, any car you add to your garage and modify will stay in the list indefinitely, and unfortunately the list isn’t sortable. So how do you get rid of cars you no longer want?
Go to your garage and select a vehicle. Instead of retrieving or modifying the vehicle, there is an option to delete it.
You can’t undo this without restoring your game, so make sure it’s the right one, and be sure you want to remove it before you click that button.