I honestly think the best way is to show them that their logic is fundamentally flawed. They need to understand
why they're wrong- not simply that they
are wrong- because they will just reject your assertion, even with evidence. This is why I confront conspiracists in a way similar to my
9/11 Conspiracy Challenge. Comparing evidence all day won't work: conspiracists won't admit that they're wrong, usually- and will usually just move right on to the next piece of crap until they finally come up with something you cannot easily explain or have never heard of- and then they claim victory... ignoring the fact that you've debunked everything up until that point and a conspiracy would make no sense.
We've had many a great debunkers show them undeniably that they're wrong- round after round... but they still repeat it. I think they believe they're right, and they will do whatever they can to maintain a theory which is self-defeating. The only way I can see around that is to actually show them that they are not being rational.