One arc of Digimon Adventure ends with a climactic battle in the Fuji TV station, which broadcast the show in Japan. It's mercilessly destroyed, although part of the architecture is used to destroy the Big Bad. As for the English version, Fox Kids was owned at the time by Fox Family Worldwide, which was a joint venture with Saban Entertainment, which produced Digimon's English version. Naturally, they averted this trope by simply dubbing the Fuji TV station as "the TV station".
Speaking of the Fuji TV station, it also occurred in several Kochikame TV specials which the building was destroyed during the climaxes. One time, its architecture was used as a wrecking ball to knock a few stories off a skyscraper.
The first episode of the OVADangaioh had the AIC building (Dangaioh's production company) destroyed by the invading bad guys.
Jackson: You know who made you a hero, right? Kotetsu: Our sponsors, sir! Jackson: Good!
A dub example. If you play a scene in episode 130 of Pokémonbackwards, you will hear James say "Leo Burnett and 4Kids are the devil! Leo Burnett!" 4Kids Entertainment is the company that dubbed the series. Eric Stuart said that he included this line on purpose, due to 4Kids not paying him for commercials.
In-universe example in Kannagi. Akiba brings a taped show for the main character Jin, because Jin accidentally taped over a show that Nagi hadn't watched yet on a VHS tape. He first hands out a Blu-ray, then when Jin mentions not having a Blu-ray player, he pulls out a tape. Nagi asks what it is, and turns out it's a Betamax tape, which Jin also doesn't have a player for. Cue the characters looking at Akiba.
Episode 53 of the second series is a scathing satire of the anime industry. Momo visits an anime production company where animators frequently work themselves into comas in the hopes they'll eventually be able to make anime with their own Original Characters. The character of the week Momo needs to help is such an overworked animator. He dies at the end.
In the animated adaptation of Excel Saga, Lord Ilpalazzo gives Excel a speech about the evils of manga, and demonstrates by tossing a handful of Excel Saga manga volumes into a giant paper shredder, and sends her out on a mission to kill Koshi Rikdo, the series' artist and writer.
Pop Team Epic: The protagonists' hatred for Takeshobo (the manga's publisher) is practically a Running Gag. After the anime was announced, the manga added in jabs at King Records and its singers, culminating in the company being a full-blown evil empire in the anime.
Season 2 of Osomatsu-san starts with a grotesque parody of the sextuplets' real life fame. The Matsuno brothers are shown lavishing in adoring fangirls and money, even though they've have gotten disgusting, fat, and even greedier than usual and their marketing team is peddling out whatever garbage they can slap together to bank off their image.
Shinya! Tensai Bakabon lives off this trope, from taking potshots at Tv Tokyo and its executives, to depicting a mobile game about the show as a cheap cash grab that makes throwing money at it a game mechanic, to criticizing the animation quality and writing of the show itself.