For 9/11, I haven't seen much of this. Eyewitness accounts are often flawed and contradictory (as they usually are) and the science is pretty solid behind the accepted explanation. Of course there are questions that can't be tested without building a few dozen identical towers and flying planes into them but I have yet to see any consistent evidence to back up the conspiracy theories, even if you ignore the numbers of people who had to have been involved and haven't spilled the beans. I see myself as being scientific and am willing to examine evidence contrary to my views but as of yet I have seen nothing compelling.
JFK is a much tougher matter to examine since the scientific nature is limited. It is also something that could have been accomplished by a very small group, greatly reducing the likelihood of a leak (of course a cover-up would include significantly greater numbers). Several groups have done tests that show that a single gunman could have done what was done. Of course this doesn't mean that is what happened but as mythbusters would say, it is plausible. It may have happened in a different manner and some of the related events muddy the water but absence of evidence supporting a coherent set of alternate events is lacking. The 9/11 conspiracies on the other hand aren't plausible.
