There are also provisions for what's called a "Bonded Title." I'm going through that right now.
The Texas procedure: Basically, you take your application, VIN information, Bill of Sale, and $15.00 to the DMV and they instruct you on how to proceed. From there, you must have the car appraised and a surety bond issued from an appropriate agency (usually, by your insurance agent and for 150% of the appraised value - not sure how much that will cost, but I've seen 1-5% of the appraised value). Take all that back to the DMV, and if your car VIN comes back as 'not stolen,' you'll receive your Bonded Title within a week or so, and be able to register & license the car to drive... after insuring and a proper safety inspection, of course. Registration taxes are based on appraised value, of course.
So basically, there will be a LOT more pain and suffering in the way of time and money involved when a 'clean title' is not part of the deal.