One of the interesting thing about the human mind ( and some of the members here), is that it seeks to idealize stuff. For instance, I've mentioned before how when we view an imperfectly drawn circle, our minds interpret as a circle, even though it may be more square or egg-shapped. Another example,( especially evident among typed internet discussions) is the way we interpret mispelled words, or the use of the wrong "to, two, too", or "there,their, they're". Our minds make the corrections required by the context so that we may understand the intended argument. It also explains why " things happen in threes". We simply group things that happen into groups of three, becasue our minds seek order. The human mind is truly awesome in this ability.
Similarly, in ANY historical event, there are many facts. Some of these facts support the general consensus, and some do not. Much in real life is random. So, in seeking to make sense of the facts that don't fit, some peolpe seek another way to order the event to fit the random facts. This is, I believe the case with the 9-11 Twin Towers conspiracy stuff. If you go into this with an anti-Bush, or anti-government, or a "our government is always lying" agenda, you will naturally "see" relationships that do not exist in the real world.
As far as the Kennedy assination goes, I have read many books over the years that purport to explain the errors of the Warren Commission Report. I have been alternately convinced of the shooter behind the fence, the shooter in the storm drain, the revision of the wounds during the autopsy, etc. The most convincing evidence to me, ( at this point, anyways) is the total lack of ANY death-bed confessions of anyone involved in the plot. Knowing human nature, I find that singularly convincing. Perhaps the same will tend to confirm, or deny the understanding of all that happened on that terrible day.