I wouldn't consider most of the books on that list to be "dark," especially not The Wounded Sky, which is one of the most idealized portrayals of the ST cast and universe you're ever likely to see.
Its also way better than the TNG episode based on it.
Steve Mollmann wrote:
Barbara Hambly's Crossroad is dark in terms of tone, kind of spooky, and features a warped future Federation.
It also has the Enterprise's bowling alley make an appearance.