I read through this thread, and I think the questions have been adressed rather well.
Tom distinguishes between two types of conspiracies- a conspiracy because the earth is round, and a conspiracy which coincidentally perpetuates the myth of a round earth. I think his argument is 100% airtight- why would anyone conspire about the geometry of an object? NASA found a niche, in a belief that people would back, and it doesn't matter to them what the true geometry is. That doesn't mean the conspiracy doesn't perpetuate RE myths, just that it wasn't specifically designed for that purpose.
Regarding flight time discrepancies, these arguments are not very solid. To say that pilots or passengers would have noticed.... These are more sociological arguments- "if the earth were flat, then this group of people would act like this". Not very solid, scientifically. My "sociological" argument in response is that if there were a valid, clear, physical reason to believe the world is round, somebody would have posted it here long ago.
The jetstream information is very appropriate. Combine the various jetstreams with the fact that most flight time eta's are wrong (so passengers are used to this), and with the fact that an indisputable FE map has not been created, and with the fact that the GPS system is controlled by space agencies... and the argument disappears.