A Zen hotdog is joke that you only got ages after first hearing in, named for an example of such a joke that I didn't initially understand.
These examples are collected from a number of people. By convention, we don't explain the joke here...
Feel free to send me any additional examples.
The original zen hotdog. I don't even want to think about how long it took me to get this, but I only twigged in 2000 or so. For ages it just seemed like a weird, stereotypically-zen thing to say.
A zen master goes up to a hotdog stand. The vendor asks what he'd like on his hotdog. He replies, "make me one with everything".
Today someone just pointed out that XFree86 was a pun on X386. That'd be, um, 1994-2002, I guess.
Fanf notes that X386 was the original name which was changed to XFree86 in 1992 when the original developer went commercial. There's a timeline in an article in Linux Magazine. This predates the 386BSD -> FreeBSD change by a year or so.
Two nuns are sitting in a bath. One says "Where's the soap?" The other says "Yes, it does, doesn't it?" (about 2 days or so)
How do you get down from an elephant? You don't, you get down from a duck. (Confused at an early age. Visions of elephant-dismounting steps made from ducks for about 10 years.)
uk.misc: ribald for your pleasure. Took perhaps a year or three.
EQDEO. 2-3 years, maybe a little more.
From Chrononauts, a Brontosaurus called Emily. About 8 months.
I only got this joke when MHF told it recently, a year or two after I'd first seen it on usenet:
A Polish (or Latvian or...) man finds a genie, who grants him three wishes. His first wish is for Genghis Khan to invade Poland, and then return home. His second and third wishes are the same and the genie asks him to explain his perplexing request. The answer? "He has to pass through Russia six times".
(A variant has the wishes including the desire that Genghis Khan change his mind when he reaches the Polish border and return home, though I think the above version makes the point better.)
The Artistic Licence. Around ten years.
pinky.sel.cam.ac.uk. About five years.
My dog's got no nose. How does it smell? Terrible.
...shouldn't that be "terribly"? And why is it funny anyway? (I can't remember how long; this was 25 years ago.)
Knurd. Since Sourcery was published in paperback.
Googleplex. Several months at least.
PartiallyClips. About a year.
Idoru. I only realized that this was a loanword when watching Perfect Blue. (I also realized I'd been pronouncing it wrong, but that's perhaps more forgivable in the absence of a pronunciation guide in the novel.)