Wow, I never realized how many hidden non-Trek references there were in the books. Sadly I don't think I've ever actually picked up any of them myself, unless of course they've already been pointed out to me.
I'm not sure what it takes, because I've caught a few, but the Hynerian and Mal Rennols
refs flew by me when I was reading them. And KRAD implies another Farscape ref in Demons of... *flips through book*
Ones I remember offhand: I was tickled by the "you don't know how to use the intercom" West Wing exchange in Articles of the Federation, the reveal of Ripley's aliens in Mission Gamma: Cathedral, and Xev Chiana (Lexx and Farscape!) in Genesis Wave.
Someone pointed out a Dr Who reference in Ishmael and one of Diane Duane's early Trek books.
^ Which is why I endeavor to keep them subtle and small. The people who get it get it and move on, the people who don't don't even notice.
Exactly how it should be. Includes non-joke textures too. It enhances the reading pleasure of those who make the connection, but it's enjoyable and understandable to all.