One of the most prolific producers of annotations for their Trek books (maybe even the only author to have done annotations for every one of their stories?) is Christopher L. Bennett, who has now posted the annotations for his most recent Trek book, Department of Temporal Investigations: Forgotten History. Naturally I recommend you read the actual book first; partly because you'll spoil it a bit if you don't, but mainly because it's so darned good! But once you have read it, go forth and find out more by reading the annotations too.
If you're curious about annotations for other Trek books, Memory beta has a handy page listing other examples. I wonder how long it will be before Pocket Books find a way to make these official extra features on ebook releases? It would be a great way for them to promote referenced books, and would make for an interesting interactive feature.