Wheels:
One of the most common variations is the wheel style. Sometimes a car (usually an early casting) can be found with the same paint scheme, but with a different set of wheels. Other times it may have mismatched set of wheels. Both of these variations can also be easily faked and do not affect the value of the car. This applies to the Turbo Wheels and Super 4x4s as well. I have seen one car with a wheel on backwards. While not easily faked, I doubt this increases it value at all. I have yet to see different wheels on the same axle, but they may exist as well. 

Body:
This type of variant is better known as a casting variation. The molds may have differences that may alter the looks of the car. Sometimes this is almost unnoticeable, other times it is very obvious. While it is best to ignore the very slight variances, the obvious ones such as the grill on the '64 Corvette should be accepted as true variations. These variations may or may not increase the cars desirability. Occasionally, a car can be found with the same paint scheme with or without a street rod engine, such as the white with red top '55 Corvette. This can affect the value and desirability of a certain car. Sometimes a bad factory mold may cause the body to be missing a section, have added globs of plastic, or just be lacking in detail compared to other examples of the same casting. I consider these variances worthless for the most part.

Paint:
The most common paint variation is the tinting. This usually is very slight and varies from batch to batch during production. For the most part, this does not add to the value or desirability of a car. The paint scheme could have been used in different packages, and additional variances may be found between two cars with similar paint schemes. Examples of such would be the color of the cover on the black Porsche 356 Speedster, or tail lights on the yellow Datsun Pickup. I believe these should be treated as separate variations in a collection. Missing paint is one of the more common paint errors. I have found many cars where normally painted areas were left unpainted. Along the same lines is the misalignment and double spray variations. A misalignment is when the details are not where they are supposed to be on the car. Some misalignment variations may also have a double spray variation where one of the details is duplicated on the vehicle. These last three types may not add to the desirability of a car.