There are actually two authorised crossovers between Starship Exeter and Star Trek: The Animated Series here:
HOME IS NOT A PLACE
http://startrekanimated.com/exetercomic.html
FOR DEATH OR GLORY
http://startrekanimated.com/tas_comic_si_main.html
Exeter was such a good show and it brings great nostalgia, especially The Savage Empire which I think was the first full-blown TOS fan film with replica sets.
I am surprised that Continues and Starship Farragut never attempted a full crossover when they were together with the exception of Captain Kirk's visit to the Farragut. You had two crews under one roof which they could have taken advantage of. With Farragut Forward hopefully coming I would have liked them to have done kind of a 'Star Trek 2.5' movie with the crew of the Enterprise, but I guess that's prue fantasy
Ironically the most well-known Trek crossovers were between Hidden Frontier in California and Intrepid in Dundee - two groups divided by both the Atlantic and most of America!!