Oh, that's tough. The traps in Raiders are so classic, perfect for suspense and that danger-lurking-in-every-pool-of-light feel. In Temple, the Spike room is my favorite scene (What with Shorty shouting in Chinese and "Hurry, Willie!"; Willie screaming that "They're in MY HAIR!"; Indy cringing as the spikes descend and telling Willie to shut up... just one big happy family.
*Another reason I could never see Willie & Indy together). And in Crusade, I enjoyed how the traps all had a riddle behind them.
That said, I think my favorite of all of the traps would be "The Path of God-- only in the leap from the lion's head can he prove his worth." The reason I favor this over all the others is that it's the first time a trap or challenge forces Indy to abandon formidable strength and common sense entirely-- it calls for him to take a true leap of faith, one of trust in a Being he may or may not be so familiar with. Indy shows his true spirit by taking this leap, letting go of what seems to make sense for what his heart and soul tells him to be true.
"It's a leap of faith... oh, geez..."
One of my favorite moments in the trilogy is when Indy takes a deep breath and extends his foot to take that first (and perhaps final) step, knowing that what he is doing completely defies reason... and then the moment when he steps onto the bridge, proving that in his quest to save his father, Indiana Jones has "proved his worth."