If you're only talking about Life of Brian, then the scene with "romanes eunt domus" is one of the funniest to me, but it's hard to choose just one. There is Terry Jones speaking from the window as Brian's mother, scene with naming all the political parties, haggling scene, messiah in a trench, stoning scene, what have Romans done for us... The whole frickin movie is the funniest scene to me. It's the same with the rest of their work, but I don't find Jabberwocky as funny, probably because it is not made out of various sketches as much as their other films are.
Romanes eunt domus

Meaning of Life when the roman catholic's must sell their children to medical research because, as the song says, "Every Sperm is Sacred".

Hard to choose, but I think my vote goes to the "Sermon on the Mount" scene from Life of Brian: http://www.youtube.com/watch?v=XiDmMBIyfsU
"Blessed are the cheesemakers"
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What is your funniest scene from Monty Python?