People here probably won't like my theory on the subject.
I honestly do not think it was terrorists, because if it was terrorism you'd have the organization responsible for it screaming that it did it, at the top of it's lungs. Heck if it was even a serious possibility you'd have terrorist organizations lining up to try and take credit even if it wasn't. Terrorists want things loud in order to spread fear, they don't just quietly disappear things.
Outlandish theories like how aliens got them, or something like "Lost" happened for real are not bloody likely. I mean in theory you can't 100% disprove Aliens, but you can't prove they exist either, and really I don't give credit to the really far out fringe theories at this point.
This leads to the big question of how a plane could disappear, and my theory is that it didn't. I think the first responders found it, but there has been a cover up, and perhaps with time we'll see cracks appear in this.
My basic theory at the moment is China shot it down. China has been increasingly belligerent about expanding it's sphere of influence, and even extended it's threat to civilian aircraft. Obama and company have told people to comply with China's directives to avoid an incident even if they dispute China's territorial claims. For the most part I think this end of things has just been posturing on China's part, but I wouldn't put it past some hothead in their military to have fired on a civilian plane. Given the "peace at any price" attitudes of the west, and China not being quite ready for an offensive war (or wanting to be seen as aggressors at this point) it's possible that those responding to the plane have been collecting and hiding the wreckage to avoid making it clear what happened, which is also why we've seen some 'false alarms' where people have allegedly found plane doors, oil slicks, and similar things which were later "debunked", since after all no clean up like this could ever be entirely air tight.
Now of course a lot of people are probably thinking "Therumancer, you just don't like China's policies" and that's true, I do not. But then again I don't like terrorists either, and haven't exactly been expressing positive opinions of Muslim culture. If I was just generally warmongering that would be a more popular place to point a finger. My theory (and that's all it is) is largely based around who could destroy a plane so suddenly, and why the incident might be concealed. China stole a lot of US missile technology (Thanks Clinton) and with current stealth tech a civilian plane might not even see a missile coming on their radar or whatever unlike Hollywood.
Again it should be noted that part of my theory was that this was a hotheaded action, not one intended by China which is why there would be a coordinated effort to conceal what happened and prevent what would be at least a major military incident. Something made easier by the fact that there were only like 3 Americans on board.
It's not a perfect theory of course, but better than say Aliens or some kind of "Bermuda Triangle" type incident... and to be honest the way it's turning out so far we might never get an answer people will accept. I'll also say that while belligerent other nations like Russia haven't been belligerent the same way China has in this particular area, and while I'm not a big fan, I just can't see Putin or a hothead Russian commander firing on a plane like this, the way I could see China doing it given it's recent border aggression. Russia is interested in it's former empire and territory and potentially threatening Europe, where China has been the one screaming about air space, oceanic territory, and it's rightful sphere of control. This also happened I believe around US territories where China has been harassing civilians by going after fishing boats with water cannons and such already, which means I could easily see someone doing this kind of thing taking it too far and blowing up an airliner (just as I've been waiting for China to actually snap and start machine gunning the crews of civilian fishing vessels, instead of just blowing the crews overboard with water cannons).