In the cartoons, there have been no direct crossovers(save for the afformentioned Season 3 episode "Only Human"), but there have been a few references:
In the G.I. Joe episode "The Gamesmaster", at the begining their are small robots fighting each other. They somewhat resemble Optimus Prime and Shockwave:





"Dinobot Island" was technically created over in G.I. Joe, in the episode "Primordial Plot". This episode had Cobra Commander doing a Jurrassic Park and cloning a small army of Dinosaur's, or something to that extent. The animation models look surprisingly similar too:


In the TF Season 3 episode "The Big Broadcast of 2006", there was a show called "Space Age Jack", and one of the characters announed loudly "Yoooo Jack!!!"
In another Season 3 episode, "Dweller in the Depths", Wreck Gar shouts "Yooo Joe!".
Last but certainly not least(that I know of, or can think of right now), there's the revlation that Marrissa Fairborne is Flint's daughter! A "hologram" of Flint appeared in the TF Season 3 episode "The Killing Jar", and he had the same voice actor as Flint from Joe. According to the TF Wiki, Flint Dille, the writer/story editor for Transformers, did indeed for this to be a reference/crossover.