Why is the S-duct intake on the Tu-154 uniquely oblong?
This doesn't fully answer the question, but the B727-100 also had an oval engine intake.

AIRLINERS magazine Sept/Oct 99 edition: 

"The oval shape inlet on the 727-100 series was changed to a circular design on the stretched 727-200. This was a direct result of the new aircraft's longer fuselage. In flight, the increased lengths from the nose to the center engine inlet increased the thickness of the "boundry layer" of air on the fuselage forward of the inlet. This would have caused aerodynamic "blanking," or disruption of airflow into the center engine, without changes to the design. The circular inlet allowed a smooth flow of air into the engine, as it elevated the bottom of the inlet away from the fuselage boundry layer and into the air stream."