Well, since it seems we're generally agreed that references would be ok as long as they make sense and don't require knowing anything about where they came from for the plot or subplot to work, I'll ask this related question in addition to the opening question: So, what references to the novels, comics, or STO would y'all like to see in such a new series and what references or type of references would y'all never want to see?
Since it's the novels that get to really flesh out the Trek universe, I'd like to see their species' backstories used. The Vulcans, Romulans, Klingons, Breen, Cardassians etc all have rich cultures which never come across on TV or film. If you're gonna make an offhand comment about them, you might as well take a detail from there.
It's worth pointing out here that the new movies referenced old novels (Kirk's parents' names, Vulcan lore), current comics (the "Mudd incident" and the dead tribble) and the recent videogame (Gorn octuplets)