Humour in music videos, outside of actual standalone visual jokes, comes in the form of either parody or pastiche. While similar in format, a homage is usually more of a love letter to the original text and is not meant to be enetertaining in itself. Intertextuality is a form of an inside joke, as referances are inherent in their nature that not all viewers will "get it".
A parody is has a more acerbic tone than pastiche, as it makes fun of certain features or stereotypes of other media texts. It encourages the viewer to laugh at, rather than with, the original text. Parodies are usually less subtle than pastiches, as they can go as far as to be an entirely different song with the same instrumental.
The Beatles Live Rare - Smack My Bitch Up
A simple but effective parody of The Beatles' family friendly image, overlaying the less upbeat Smack My Bitch Up (The Prodigy) over archive footage of The Beatles preforming live. A main benefactor of why this video is so effective is the care that has went into syncing the song and video together, making it actually look like they are playing the song. The original crowd reactions (girls screaming and fainting etc) remain, seemily euphoric at hearing The Beatles preform their classic hit.
Macklemore - Thrift Shop Music Video (Parody)
This video is made under the pretence that the viewer has an understanding of both the original song and its music video. It both alters some scenes from the origianal video and changes the lyrics to tell its own story, again based off of the original song.
Another method of introducing humour into videos is to take amplification and illustration to their limits. This works especially well if the song in question either is humourous or has a self contained narrative.
An example of this would be Tenacious D's Tribute, which is a visualisation of the lyrics, word for word. The only thing the video adds is some slight context, with the song being performed inside a photo booth. It uses special effects to amplify the lyrics. This also has the effect of linking the song to the video, giving extra meaning on that line to those that have seen the video.
In typical Beastie Boys fashion, the video for "3 MC's and 1 DJ" is as entertaining as it is promotional for the song. The video opens with the aforementioned 3 MC's stood in the above pose perfectly still, cross-cutted with the DJ holding a record and walking down the street, going into a building and putting the record on. There is about a minute and a half of watching the DJ walk and the MC's stood still before the music starts. After the music starts, there is very few camera angles and it is all shot in the same room, meaning this style of video making would be replicable in our own production.