Yes, absolutely a plane crashed into the Pentagon on September 11th.
To address the claims specifically.
but did not even scuff up the grass
Do you know what airplanes do? They FLY. That this is even a claim is absolutely ludicrous and seems to be grasping at straws... Mike J. Wilson does a nice reconstruction of the crash that shows this gravity defying feat quite clearly. Not only that, it has actual photographs and video from the Pentagon that not only show the effects, but even show airplane debris.
In case 9/11 truthers are attempting to draw a comparison between a crash into a structure at high speed and these "examples" of crashes, they are being deliberately deceptive. The "crashes" they are using as examples happened under much, much different conditions than the 9/11 crash. I would suggest maybe the Payne Stewart crash site would be more indicative of a crash at high speed.
(Image source, South Dakota Community News)
Or Maybe another crater like this Tupelov crater in Iran:
(Image Source, USA Today)
Of course, the general nature of most pilots is to NOT crash! So if they are able to do anything when they realize things have gone into a total "furball", they will do everything to preserve their lives (like attempting to get to an appropriate speed, attitude, orientation, configuration, etc.). The extremists on-board the aircraft were not taking any of those actions, and were trying to do as much damage as possible. Thus they had throttles up, and were going at very high speed in a clean configuration when they crashed into the Pentagon (and the WTC for that matter).
The pictures shown in the question are from crashes near the landing or take off phase, which has totally different parameters (and even a movie set which isn't even a real crash...). Again, highly disingenuous of the truthers...
like a lack of broken plane parts
Now, there is the claim there are no parts. The video by Mike Wilson shows photographs of numerous parts, so that is plainly an outright lie of omission. The photograph that truthers display as an "example" is from a long distance, and does not show the entire site either. Here are four pictures that DO show aircraft debris:
(Image Sources, James Randi Educational Foundation, from other sources)
Furthermore, truthers seem to be wholly unfamiliar with materials science, physics, and structures. They do not seem to know what happens when an aircraft is driven into a wall at high speed? Here is a wonderful example of a test conducted by the government many years ago with an F-4 (YouTube Video taken from a Sandia Test as referenced in Sugano, T., Tsubota, H., Kasai, Y., Koshika, N., Orui, S., W.A. von Riesemann, D.C. Bickel, M. B. Parks, (1993a), “Full-scale aircraft impact test for evaluation of impact force”, Nuclear Engineering and Design, Vol. 140, p373-385.). As one can plainly see in that video nearly a decade before 9/11, the plane is quite effectively obliterated, only leaving very small parts.
Now, if anyone sincerely wishes to find out more about what actually happened, and wants to stay with actual facts (as opposed to manufactured ones, or plain old delusions), I suggest they visit the James Randi Educational Foundation. Not only are there plenty of discussions that debunk these same tired old arguments, but one can ask the same questions again and again. And you'll get the same answer, because people demand EVIDENCE, not cherry picked half-truths. Much like here.
And just for giggles, I think this comic by XKCD touches on why I have such disdain for these nutty conspiracy theories.
(Source: XKCD [as if you couldn't tell])