Re: your favorite standalone novel?
TOS : The Final Reflection
TNG : Q-Squared
DS9 : 34th rule
NF : Once Burned
Also, "Federation" doesn't truly belong to any one era but deserves to be on any "best of" list for me. "Where Sea Meet Sky" is a great pike book, and the six book "Errand of Vengance/Errand of Fury" is my favourite mini-series.
In defeat, malice. In victory, revenge.