To me, the fighting game genre seems to have had a ton of crossover releases and guest appearances since forever. A more recent (2012) "fan" created game that I enjoyed was the "Megaman VS Street Fighter" release which was announced at the 25th Anniversary of Street Fighter event, celebrating 25 years since the official Japanese release date of "Rockman", the Japanese title of Mega Man.
Although not fan created, I personally remember playing X-men VS Street Fighter in the arcades back in 1996