I can strongly recommend Donnington and Coventry. Both are much larger collections than you would ever imagine before you visit them and both representative of their subject.
Of course a lot depends on what your interests are, if you are an out and out race fan and have no interest in road cars Coventry might not be for you but they do have the two fastest cars in the world Thrust 2 and Thrust SSC as well as the more transport oriented exhibits.
To wander off topic a little another excellent museum is the RAF Museum at Cosford who have a huge collection military aircraft but of course if you have no interest in military aircraft (not unlikely as you posted the question in a motorsport forum) that may not be of much use to you although they do have a mini, a VW beetle and a trabant in the cold war building.
