While I haven’t read it myself, I know there was a my little pony comic that made the rounds a while back with the mads in it! I don’t know the issue myself though, I just saw it around.
Another one I haven’t actually read, but one of the Archie Comics Sonic series (issue 52, if google is to be believed) had Crow and Servo in it
On an old Team Fortress 2 Update page (from the Replay Update in 2011) the site has a graphic of the mercs watching the update video and Scout is making this pose, which I have a feeling was intentional
In Star Wars Tales #1 (1999) we get to see a stripped down version of the ‘bots as well.
Lastly, while not TECHNICALLY an MST3K reference, I’m including it because I love the series, and, let’s face it, Manos is synonymous with MST3K, check out the Hand Witch (a witch who has the magical power to control hands) from Gravity Falls in the episode “Little Gift Shop of Horrors.”
oh, and while not technically a reference, a couple Cartoon Network shows have had Joel and Bill on them, and im willing to guess it’s because somebody on the respective crews might have been a fan given they don’t tend to do much voicework normally. Joel played Mayor Dewey for Steven Universe’s run, and Bill played Perry the Parasite in Infinity Train recently.
Unfortunately I don’t have a lot of my comic collection anymore, but there was one issue of the anthropomorphic comic Shanda The Panda with a Mistie gag. Shanda worked in a movie theatre and there was a silhouette illustration of her as an usher leaning into a row with a flashlight and addressing the MST3K silhouettes. Her line was to the effect of “Excuse me, but I’ve had complaints of talking.”
There’s a Star Trek/MST3K Easter Egg. On Star Trek: Deep Space Nine, there is a listing of stores on the Promenade. Among them, as confirmed by Memory Alpha, one can find Tom Servo’s Used Robots.
They even took it a step further by making sure it was included in the Promenade Directory in Star Trek Online. I also got a kick out of “Spacely Sprockets” – maybe Tom Servo got to repair Rosie for the Jetsons.
In an episode of Arrested Development season 4 (varies if you watch the original cut or Fateful Consequences recut), Joel and the bots are watching a 90s version of Fantastic 4 with Tobias’s girlfriend DeBrie as the Invisible Girl