I have heard the theories around the Pentagon incident on 9/11. They are quite popular. They can be blown away pretty easily though due to the large amount of proof such as the flight data recorders, debris fragments, confirmation that the Islamic hijackers were on board, and so forth.
https://en.wikipedia.org/wiki/American_Airlines_Flight_77
Really it's an easy one to figure out. Supposing it wasn't an aircraft that struck the Pentagon a major question would have to be asked about what happened to American Airlines Flight 77. Boeing 757s don't just disappear without anybody noticing.
A theory to that (without any evidence that I've found but it is still plausable), is that all of the airplanes on that day were routed to air-force bases, passengers were sent to a military prison like Gitmo or executed, and it was drones that hit the towers/pentagon.