Depends on what sort of lot your talking about. Is it a residential/apartment lot? Shopping center?
As long as you haven't violated the posted rules for the lot than your vehicle cannot be towed, however, it's very difficult to fight this sort of thing. It isn't their responsibility to notify you if your vehicle is towed, there should be a tow-company number that's listed at the lot. Or talk to the security/lot attendents to see if they called any tow-trucks during the specific date/time. As a matter of rule, your license plate number/vehicle make/model will usually be recorded by the lot attendent.
Unfortunatly, tow/impound companies are real hardasses and even if you threaton to sue them they won't give you your vehicle until you pay the tow and impound fee (Which is calculated by the day) It's best to pay the fee, and if you want to sue them in small claims court later you can do so...but you'll have to provide some sort of proof that they towed you wrongfully.
They are responsible for any damage to your vehicle during the tow and storage. Take a digital camera with you when you go to the lot.
If the vehicle turns out to be stolen, or you can't find it at the local tow lots, check with your local police department. Tow companies will often radio in a vehicle license plate/make/model to the police just so no one comes screaming that their car is getting stolen. Call your police non-emergency number and see if they have any reports of your vehicle.
Hope this helps.,