Ghostbusters: Times Square! has no reason to not be canon to the main reality - the wiki just assumes it's not due to the lack of a connection and it's origins. It was supposed to be a prequel to the video game until references were cut, so October 1991. The manga could be canon too since it's set in the 1990s post-Ghostbusters II. We'll say before The Other Side.
Ghostbusters: Legion, unfortunately, is set in a world where Ghostbusters occurred in 2004. That would place it in a unique reality.
The X-Files: Conspiracy could be set in Dimension 50-S, since it's only a few years after Sanctum of Slime and the Ghostbusters barely aged in that reality, or as a continuation of Ghostbusters: Legion. In any case, I'd probably put it in a miscellaneous section on it's own as "X-Files Universe".