While this doesn’t count as ‘humor,’ I still think it’s funny:
2 Kings 2:23-25
Some kids are making fun of bald-headed Elisha, who curses them in the Name of the Lord.
The Lord hears Elisha’s plea and sends two bears to make short work of 42(!) kids!
(Just 42, that’s not a factorial.)
Arguably when Christ calls Peter ‘the rock on which I will build my church’ he makes a pun on petros [rock]
I think in the Living Bible Elijah speculates that Baal may be on the crapper.
For the record, the “kids” in that episode were little children but a gang of snotty teenagers trying to goad him into losing his temper. In addition, it’s implied that the “bald-head” insult wasn’t just meant to make fun of his follically-challenged cranium but also suggest it looked like a circumcised part of the male anatomy (i.e., they were calling him a dickhead).
FTFM
Probably not what you’re looking for, but Robert Crumb adapted the Book of Genesis into comic book format. Literal and surprisingly respectful, it has lots of sly, subversive humor. It’s also the best-selling thing he’s ever done, which he has got to have noticed. No jokes as such.
I’m not sure whether it counts as humor or just scathing sarcasm, but I’m a big fan of Job chapters 38 to 41.
In particular, after asking a whole string of questions that no one can answer, like what the origin of the Earth was, the Lord says (38:21) “Surely you know, for you were already born! You have lived so many years!”
I always found this humorous:
Matthew 5:22 (NIV) Jesus says: “But anyone who says, ‘You fool!’ will be in danger of the fire of hell.”
Then a some chapters later (23:17) Jesus tells a group: “You blind fools!”
Oops.
On one of the many occasions when the Hebrews are griping at Moses, they are recorded as asking “Did you bring us out into this desert to die for a lack of graves in Egypt?”. This seems like the sort of sarcastic griping characteristic of Jewish humor to this day.
Numbers 11:18-20. The bold section is what cracks me up.
18 “Tell the people: ‘Consecrate yourselves in preparation for tomorrow, when you will eat meat. The Lord heard you when you wailed, “If only we had meat to eat! We were better off in Egypt!” Now the Lord will give you meat, and you will eat it. 19 You will not eat it for just one day, or two days, or five, ten or twenty days, 20 but for a whole month—until it comes out of your nostrils and you loathe it—because you have rejected the Lord, who is among you, and have wailed before him, saying, “Why did we ever leave Egypt?”’”
How about wordplay?
Matthew 23:24 “You blind guides! You strain out a gnat but swallow a camel.”
“Gnat” and “camel” in Aramaic are respectively “galma” and “gamal”, so there’s a bit of wordplay there.
I can’t find the reference now, but I believe there is another component to the statement that sharpens it. Apparently some Pharisees literally strained whatever they were drinking through cloth so they wouldn’t swallow gnats or other small insects, which are considered unclean as food. But camels are also unclean, so the metaphor is that they were avoiding tiny uncleanliness but accepting major uncleanliness.
I was all set to cite Elijah talking epic smack to the priests of Baal, which is indeed pretty damn funny. 
I believe you actually meant that Jesus’ nicknaming of Simon as Petros (meaning rock or stone) was “because you will be the cornerstone of my church”.
He wasn’t making a pun of an already-existing name: he was giving the name.
Well, if you subscribe to the theory that “Get thee behind me, Satan” was a first-century euphemism for “Kiss my ass”…
Without irony or facetiousness, I say that the book of Jonah is intentionally hilarious.
The notion that something that was perceived as a sacred text would contain jokes is just absurd. It’s amazing what people can read into things.
The notion that it wouldn’t contain jokes is even more absurd.
If we are created in the image of a given deity, and we demonstrate a sense of humor, than the deity in question must also enjoy a good laugh every once in a while.
Thus pandas.
Out of curiosity, do you also believe that the Quran contains jokes?
The Prophet (peace and blessings of Allaah be upon him) had no problems with jokes, as long as they were respectful to Islam and were not used to mock or belittle others, for that path leads to hatred and grudges.
I am not familiar enough with the Quran to know of any jokes or wordplay in it, but I would not be surprised if Mohammed just didn’t care to write down any. he doesn’t seem to have much of a sense of humor himself, nor did he inspire humor in those around him.
As the Bible was written by many hands it is certain that at least a few of the writers were witty if not actually funny.