I've been digging around for a bit. Snopes and several other sites do have "debunkings" of the missile theory - but I haven't yet seen a single image that shows anything that resembles a 757 jet airliner anywhere even near the Pentagon. There is a series of photos on a CNN site that show an explosion and flames and aftermath, but again, nothing resembling anything - not even wreckage - of a jet airliner. The CNN page even states that the airliner hit ground before hitting pentagon. EVEN STILL... there is no wreckage - no wing bits, no tail bits, nothing - that resembles airliner.

Taking it a step farther - in the WTC footage you could clearly see that one of the engines went clear through the second tower and out the other side. This would suggest we'd see impacts from the jet engines on either side of the main impact... and there are none. Even if the plane bounced before hitting, the wings would have sheared off, either on bouncing or on impact with the buildings, and there's no sign of that either.

I read a claim that the fusilage made it through almost to the core. Surely upon hitting steel re-inforced concrete the cockpit crumpled like an alunminium cigar tube in a hydrolic press, even as it began to enter the building.

If the state department or war department had photos clearly debunking this you'd think they'd have published them on their own.