I liked how Parker and Stone handled it. As has been pointed out, they did a good job jabbing both Lucasberg and the people who railed on Indy 4 so hard. It was mediocre, but far better than the movies that have been knocking off the Indy series like National Treasure and The Mummy. Plus, complaining about the fridge scene or monkeys seems petty. The reasons I thought it was a downgrade were the over reliance on CGI and the lack of focus on Indy (Ford showed he was definitely capable, so why didn't they let him run with it?).
As for favorite rape scene? The stormtrooper one. Though the parody of The Accused was inspired (especially the cameo from Major Toht).