Re: Into Darkness and the novelverse [SPOILERS]
Deneva and V'Ger already been addressed in the comics. I haven't read any of them myself, but I'm pretty sure I've seen references to V'Ger being in the Nero comic series, which covers what Nero was up to between the opening of the movie and the main story. They did an adaptation of Operation: Annihilate as the 5th and 6th issue of the new ongoing comics series.
Over the course of many encounters and many years, I have successfully developed a standard operating procedure for dealing with big, nasty monsters. Run away. Me and Monty Python.
Harry Dresden - Blood Rites (The Dresden Files #6)