I can't say there are any that I felt were overused, but there have been jokes I've written in my comic only to discover a close friend of mine made the same joke. This happened a lot when I was still doing fancomics (and is part of why I stopped doing them, because it felt like a rush to see who could make the joke and get the views first, and there was honestly other people who were much better at their execution than me so I felt like I wasn't really adding anything new)
I guess the most recent case of this is with my comic Paisley Brickstone, I wrote a joke involving a character twirling keys on their fingers only to have 'em fly off in a crazy direction for a later chapter that isn't released yet (spoilers for flying keys), and then shortly after starting to actually plug and network on the forums, one of the first comic buddies I made ( @phenylketonurics ) had the same joke in a gag comic they made for their series ( There's No Such Thing as Jason ). It was literally the very first comic I read on tapastic, and it was only a week or so before that I wrote that part for my own comic so of course the first thought in my head was "WOW I SHOULD TOTALLY WRITE THAT JOKE OUT PEOPLE WILL THINK I'M COPYING THIS AMAZING ARTIST'S STUFF" despite being an extremely unimportant thing in both of our series. I haven't even mentioned this to them yet, so now Phen gets to see this truth being spilt.
I did not end up writing that part out, though, it's still there, it's still happening, and the only people who will make the connection are me and anyone who reads this post and happens to follow my series and somehow remembers this months down the line when that part actually pops up.