Q will ally himself with the Federation against the Borg and Cybermen
Qs are time lords. Gallifrey is the Q-Continuum.Obvious, really.
Gene Roddenberry is a Time LordHence why Star Trek is able to simultaneously exist in a parallel universe and be a TV show that Rose (and Izzy) have previously referenced.
Guinan is a Time LadyGo reread her conversation with the Doctor, it might as well be official.
The events of the crossover indirectly lead to Star Trek: First Contact happeningIt's all too easy to extrapolate from the end of the final issue, with the Borg stating that they intend to master time travel as a result of their experience with the Cybermen and the Doctor. Kinda makes the whole thing a bit of a Nice Job Breaking It, Hero moment for the Doc...
The reason the Cybermen in Nightmare in Silver are like the Borg is due to this encounter
The reason Star Trek is Fictional in the Whoniverse is because the thoughts of the writers tuned into events of the other Universe