By choice, the vast majority of recent Trek novels are all in the same continuity (with the occasional mistake here and there, just like the TV show, but nothing egregious.) This includes all the DS9 novels.
Occasionally, there is a project that, for whatever reason, is chosen to be outside the normal continuity. If I recall correctly, the only ones lately have been the Crucible TOS trilogy (an anniversary trilogy that just focused on TV show continuity); William Shatner's long series wherein Kirk is resurrected after Generations (usually called the Shatnerverse); and the TOS novel The Children Of Kings. Also, New Frontier - a long, ongoing series that started in the late 90s - has a vague relationship to continuity, basically doing its own thing but with some of the other books referring to it. Its last novel seemed pretty out there, though, and might not be reconcilable with the rest.
Everything in the giant flowchart in my signature is part of the large-scale continuity. You'll see it called the "LitVerse" a lot around here, and the vast majority of it is freaking awesome.
And if you're worried about all this massive continuity getting overturned, Pocket's license to write Trek isn't going anywhere any time soon, and there seem to be no plans for any screen productions in the Prime universe at all right now. People make a big deal about how Star Wars's EU is technically "canon" while the Trek novels aren't, but in practice it works out to exactly the same thing - both novel series stay consistent within themselves, but can be overwritten by new screen productions at will. Since SW has new screen productions coming but ST doesn't, the ST continuity is probably safer than the SW one, regardless of what label you attach to it.