If a TNG-era Trek had a tattooed, red skinned alien in the background it could be a Thallonian. If there's a display graphic listing nearby ships, it could have the USS Excalibur NCC-26517-A on it. If something's incredibly tough, someone could say, "That's tougher than a Brikar's hide."
Those are the kind of New Frontier references that I think would work well. If the next movie mentioned "Vanguard station" in the same kind of way Regula One got a shout-out in STXI (when assignments were being called out in the academy hangar), that would work well, too. Little things that make fans' ears prick up and think, "I know that!", but not things shoved down our throats.