* In the Episode 'The Crime Machine', Holmes freaked out when Watson got shot in the leg. In the Canon story, "The Three Garridebs", Watson was shot in the leg and Holmes freaked out there. So, it was really a case of deja'vu for him.
* The reference to Moriarty being a Star Trek fan makes a lot more sense when one remembers in the original canon, he was an astrophysicist.
** And considering Moriarty "guest starred" on StarTrekTheNextGeneration, here he's just returning the "favor", as it were.