In the olden days (the nineties!) when I read some of the novels, they were always made to fit with the TV series and films rather than form their own continuity, so there was rarely a massive conflict there. Now with the more "expanded universe" continuity in the novels, anything that happens in the prime universe after Nemesis in any future series or films will probably contradict those. Which is fair enough. I like the idea of that internal continuity, because I feel it rewards the loyal readers and makes for a richer set of characters. On the other hand, from my point of view it makes me almost certain to never read another Star Trek book again! I can't commit to picking up everything published to keep up with the story. I used to like the short story anthologies, because you could just pick them up and enjoy. Shame they cancelled the Strange New Worlds series.
JJ's upcoming Star Wars sequels will almost certainly render Star Wars' novel continuity null and void, which will be quite funny to watch from the sidelines.