Cast from a show or movie are giving commentary using the characters they play as their voices.
Rutt and Tuke provide a rather humourous commentary for Brother Bear, complete with the option of having silhouettes similar to MST3K occasionally appear, and there's even a point where the pizza delivery guy walks into the recording booth to deliver a pizza they ordered.
Fantasia 2000 has a commentary track highlighting each individual segment. For "The Sorcerer's Apprentice", Roy Disney is joined by Mickey Mouse, who provides insight on the filming of the short. Later, Donald Duck crashes the commentary track for his segment, "Pomp and Circumstance", but mostly he complains that he didn't get a song to sing.
"The King of Town" has commentary by Strong Bad. "The Search for the Yello Dello" has commentary by Strong Bad, Homestar, and Strong Sad. "Experimental Film" has commentary (hidden as an Easter Egg) by the directors Strong Sad and The Cheat... and Strong Bad and Homestar show up to crash it.
Many, many of the shorts on the DVDs feature commentaries from a variety characters primarily Strong Bad and Homestar.
"Store Wars": Mac, Bloo, and Frankie give a commentary; Mac and Frankie attempt to get Bloo to sign an apology letter for the incident(s) in this episode for Frankie to go back to shop.
"Mac Daddy": Cheese gives a commentary throughout the episode "Cheese Spills the Beans".
Most of The Muppets' movies have the characters providing commentary.
In the SpongeBob SquarePants episode "SpongeBob vs. The Big One" Plankton gives a commentary titled "Plankton's Special Sinister Commentary". Also similar to MST3K.
In an episode of American Dad!, Klaus pretends his life is a DVD and he's supplying the commentary track. Late in the episode, he starts talking over a scene he's not actually in.
At least one episode of The Boondocks has commentary by Uncle Ruckus. Doubly hilarious because it's "Return of the King", the anvilicious MLK episode, and consists mostly of Ruckus doubling down on everything he said during the episode.
Making Fiends: In the DVDs of the web series, there are alternate versions of each episode. A few of them have commentaries by characters.
"Charlotte's Fist Day Part 1: New Student" by Charlotte and Vendetta.
"Charlotte's First Day Part 2: Show and Tell" by Marion.