The "riding the submarine" bit always bugged me but I think by the point it happens the movie has been fun enough that it is easily shrugged off/waved away. It wasn't TOO absurd given it would be "possible" if "certain conditions" were met, which really should have been shown in the movie but, whatever.
The "nuking the fridge" bit was just utterly absurd. The fridge survived a NUCLEAR explosion first of all. (I don't care if the fridge was made out of adamantium it wouldn't have been tossed around like a helium balloon in a stiff breeze like that.) Secondly even if it COULD survive the explosion and even if the lead lining in the fridge was enough to protect Indy from the radiation the thing got slammed around so much "landing" that Indy should have been liquefied by it. That bit (and the multiple waterfalls bit later on, and the Shia and the fencing on the racing cars in the forest and the swinging in the treets and... UGH...) was all simply demanding too much hand waving and suspension of disbelief for utter ridiculousness. What's worse the movie wasn't good enough to shrug all of that off.
The U-Boat thing was silly but only because the "explanation" for it isn't in the movie. The using the life raft bit? Silly and absurd, sure, but it "tried" to make you fall for it by making it seem somewhat plausible. It wasn't too out of line and on the surface it "makes sense."
All of that very different than that damn fridge scene.