Since, as you have noted, we have already had a joke thread, perhaps it would have been better to ask for, e.g. funniest rationality quotes or funniest LessWrong comments? Or perhaps make it more specific than the previous thread. For example, some jokes that are thought of as nerdy, math-y or intellectual are actually quite simple, as their reputation as intellectual is based on the subject matter they touch and not on the joke's "structure" itself (e.g. their humour derives from puns, cultural references, or parodies of the cultural references). In short, these are the jokes that, to paraphrase The Ig Nobel Prize description, make you think, and then laugh. On the other hand, some jokes might have mundane subject matter, but their structure may impress you more than the subject matter itself. These could be called jokes that make you laugh and then think. Obviously, there are many fewer jokes of the latter type. A couple examples that, I think, qualify, both taken from LessWrong comments:

From here

Once there was a miser, who to save money would eat nothing but oatmeal. And what's more, he would make a great big batch of it at the start of every week, and put it in a drawer, and when he wanted a meal he would slice off a piece and eat it cold; thus he saved on firewood. Now, by the end of the week, the oatmeal would be somewhat moldy and not very appetising; and so to make himself eat it, the miser would take out a bottle of good whiskey, and pour himself a glass, and say "All right, Olai, eat your oatmeal and when you're done, you can have a dram." Then he would eat his moldy oatmeal, and when he was done he'd laugh and pour the whiskey back in the bottle, and say "Hah! And you believed that? There's one born every minute, to be sure!" And thus he had a great savings in whiskey as well.

-- Norwegian folktale.

Another one from here:

"“It seems a Christian missionary was visiting with remote Inuit (aka, Eskimo) people in the Arctic, and had explained to this particular man that if one believed in Jesus, one would would go to heaven, while those who didn’t, would go to hell.

The Inuit asked, “What about all the people who have never heard of your Jesus? Are they all going to hell?’

The missionary explained, “No, of course not. God wants you to have a choice. God is a merciful God, he would never send anyone to hell who’d never heard of Jesus.”

The Inuit replied, “So why did you tell me?”

Well, the second one might remind some people a local cultural reference, but it is definitely not a part of the joke itself.