Is the September 11th the only time a plane was crashed into skyscrapers?
Intentionally with a large aircraft, yes. There was however an instance in 1945, where a B-25 Mitchell collided with the Empire State building. This however was an accident.

There have been several suicides by airplane where the aircraft was deliberately crashed into buildings, such as the C172 which was crashed into a Tampa FL high rise in 2002 or the Piper Dakota crash in Austin, TX.  There was also a case of an accidental crash of an SR-20 into a NY high rise apartment building in 2007, killing baseball player Cory Lidle.