I recently came across an interesting website dedicated to research of the events of 9-11, including detailed structural failure analyses of both towers, inconsistencies in the standard explanation of events for the day, open questions regarding the sequence of events, the cause of destruction of the twin towers, and a number of other issues. I picked out the most interesting points here (including links).

Structurally:
The temperatures that could have been reached inside the towers due to jet fuel fires is not sufficient to cause the failure of the central steel supports. Link
Fires did not consume enough of any single floor to cause a failure of floor-trusses extending from the outer shell of the building to the steel core.
The collapse of the twin towers did not progress as would be expected from a building suffering from failed supports (trusses or support columns). In fact, its collapse was much faster and more violent, involving enormous amounts of laterally propelled dust and debris. (Usually a signature of collapses caused by carefully placed and timed explosives)
The amount of energy involved in the collapse far exceeds the gravitational potential energy of the building. In addition, the symmetric collapse of the steel structure and complete destruction of the core supports cannot be explained by the collapse of the damaged floors. Link
Generally, the collapse of the towers was not consistent with the Laws of Physics in a number of ways. Link
Structural Links: One Two

Also of note, involving the hijacking:
The absence of the hijackers from the flight manifests of all of the commandeered flights.
The lack of any physical evidence, such as airport security video footage, showing that any of the hijackers boarded any of the commandeered flights.
At least 6 of the 19 named as 9-11 suicide hijackers are still alive. Link
Standard Operating Procedures involving the interception of off-course planes by NORAD were not followed on 9-11. Link Link 2
The hijackers, never having piloted any jet before, and having only very basic flight skills, managed advanced maneuvers that would be difficult even for experienced fighter pilots. Link

Other Links:
WTC Architecture


iCivilEngineer WTC Articles (See "Evidence of Explosives in the Twin Tower Collapses")

I do not mean to imply that there is necessarily any conspiracy surrounding the 9-11 attacks, but some of this evidence seems to merit further inquiry. It seems the facts (the Laws of Physics) don't add up on this one. (Yes, they should.)
But then again, what would civil engineers, architects and physicists know about this kind of thing?