Obviously there are some theories out there which are born of hear-say, conjecture, misinformation, and ignorance.
Others have not really been addressed in any serious way - and probably could not be, because no one would have written out documents.

The people who object to them, (Popular Mechanics, John McCain, 9/11myths.com) tend to point out the reasons why such and such could have physically happened the way the official version says it did, or why such and such theory is impossible.

They then also say something along the lines of it being both unscientific and and detrimental to America to suggest such things.
But how it happened is not the point, and never was.

Never mind that they were supposedly unable to find any of 4 blackboxes at the WTC center site (which are specifically designed to withstand a crash - that is the entire point of their existence - and give of a signal to aid in their recovery) but they were able to find a passport made of paper within hours - which happened to belong to one of the "terrorists"; it could happen.

Never mind that the damage to the pentagon was substantially smaller than the size of the plane which was supposed to have hit it, and that there was no sign of pieces of wing, engine or other plane parts visible anywhere on the site (or that video of the event was confiscated, or that it just happened to hit the one wing of the building which had just been reinforced and was largely empty due to the renovation), perhaps the engines vaporized but the fuselage punched through, it could happen.

Never mind that WTC 7 (which housed the FBI, CIA, and SEC - including the files on prosecuting Enron and dozens of other corrupt corporations) collapsed entirely due to fire and being hit with falling debris - unlike WTC 3, 4, 5, 6 and every other building in the area - which is unprecedented in all the rest of history. That too could be a coincidence.

If every thing physically happened exactly the way the official version says, that does not in anyway make it less likely Americans - and specifically the government - was directly involved.

If they were, we would likely never know.
They certainly had a lot to gain from it, much more than the Islamists did.

It would not have taken much.

Say a few core members of the PNAC ( http://en.wikipedia.org/wiki/PNAC , http://www.newamericancentury.org/ ), a couple high level, trusted CIA agents, and 2 or three trusted Saudi Arabians, Bin Ladens perhaps.
The PNAC is a primary think tank of the neocon movement, and includes people who have held high government positions for the past half century and other rich and powerful people, including Dick Cheney, Donald Rumsfeld, Paul Wolfowitz, Jeb Bush, Zalmay Khalilzad, Richard Perle, Richard Armitage, Dan Quayle, and Steve Forbes.

I am not saying this happened. Just consider the possibility.

Say, hypothetically, they plan what the targets should be, maximum effect, minimum actual damage, and believable. Something symbolic, but not catastrophic. A military target to justify a military response, and plenty of civilian deaths to get the American people agitated. They maybe provide limited cash, but that's it, for fear of ever being caught.

Mostly what they would have provided was the idea, what to do, how to do it. They would have wanted clues planted well in advance - for example, having the volunteers train at a US flight school, when they could just as easily trained in their own country, or a neutral one. They might have made sure to set up certain military training exercises, certain security camera angles, stuff which could seem perfectly innocent, but which would help make it easier to carry out, and easier to know who to blame. Bin Laden's original idea was to hit some 10-20 targets at once, on both coasts, but they would have shot that idea down, because they wanted to limit the actual damage. Then, through the Arab contacts, they found some people looking to martyr themselves. The actual hijackers have no idea that they are actually enacting a plan partially developed by and for the US leadership, they feel they are doing God's work by killing thousands of corrupt infidels. And the end result is the Islamists are able to up their recruiting a million percent, and the PNAC gets almost absolute power and one step closer to their stated goal of world domination.

Their principals (emphasis mine):

• we [the US] need to increase defense spending significantly if we are to carry out our global
responsibilities today and modernize our armed forces for the future;

• we need to strengthen our ties to democratic allies and to challenge regimes hostile to our interests and values;

• we need to promote the cause of political and economic freedom abroad;

• we need to accept responsibility for America's unique role in preserving and extending an international order friendly to our security, our prosperity, and our principles.

http://www.newamericancentury.org/statementofprinciples.htm

They spelled out in better detail how to achieve this in a report they released in 2000: (http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf )

"while the unresolved conflict in Iraq provides the immediate justification [for US military presence], the need for a substantial American force presence in the Gulf transcends the issue of the regime of Saddam Hussein"
"Over the long term, Iran may well prove as large a threat to U.S. interests in the Gulf as Iraq has. And even should U.S.-Iranian relations improve, retaining forward-based forces in the region would still be an essential element in U.S. security strategy given the longstanding American interests in the region".

"...advanced forms of biological warfare that can target specific genotypes may transform biological warfare from the realm of terror to a politically useful tool"

"...the process of transformation, even if it brings revolutionary change, is likely to be a long one, absent some catastrophic and catalyzing event — like a new Pearl Harbor."

This last one is most telling, since there is strong evidence that the US government, including possibly President Roosevelt, knew that the Japanese were planning the attack, and deliberately failed to warn the base because a surprise attack would better appal the American people and build their support for the war.
( http://www.thenewamerican.com/departments/feature/1999/070499.htm http://www.fff.org/freedom/1291c.asp http://www.independent.org/events/transcript.asp?eventID=28 )