In Austin Powers 3: Goldmember, one of the few moments of wit comes when Scott Evil slowly turns down his father's path of darkness. No, this in itself isn't funny, but it is amusing that Scott Evil's hair changes throughout the picture, first resembling Brian Grazer and finally, at the height of his evil, Ron Howard.
Now, of course, at the time, Mike Myers was involved in a bitter feud with them regarding Myers having left the Sprockets project just before shooting was to start, citing script issues. As a result, Myers was sued for $20 million and the suit was pending when Goldmember went into production. Not subtle, but it's as much of a dig as anything else on the list. One could argue that Myers got his revenge on Universal by making The Cat In The Hat for them, a movie so terrible that the Earth in the Universal logo almost stopped spinning.
Also making the list is the bone-headedly unfunny Siskel & Ebert clones in Roland Emmerich's Godzilla, apparently included as punishment for the two legendary film critics rightly comparing Stargate to an Ed Wood film (I guess that makes 10,000 BC a Uwe Boll film). Ebert was apparently was quoted as having said "Now that I've inspired a character in a Godzilla movie, all I really still desire is for several Ingmar Bergman characters to sit in a circle and read my reviews to one another in hushed tones." At the time, Ebert also expressed disappointment that he was not eaten by Godzilla.
And he's right. Detective Comics writer Chuck Dixon had the right idea in 1994 when they included Siskel And Ebert look-a likes, as gun-toting film critics/thugs, in an arc involving The Joker making a movie about the death of Batman. And, exactly as it should be, S & E eventually panned the movie, leading The Joker to give them 'two thumbs down' as he shot them both.
If you're going to be in a Godzilla movie, you want to be eaten by Godzilla. If you're going to be in a Joker-centered Batman comic book, you really want to get killed by The Joker. Although if I had my say, I would have demanded that I go out via Joker Venom, with a big post-rictus grin. It's a shame that Nolan couldn't find a way to plausibly include the trademark death grins in The Dark Knight, but I suppose the three corpses that are found covered in clown paint and with their mouths slit open is close enough.