While none of them have had a big effect on the universe, there have been references to things like the Selevian War, Thallonians, and Triexians. On the other hand, I don't think PAD has ever tied NF into the rest of the Trek Lit universe himself, pretty much any ties have been made by other authors.
PAD had the Excalibur-A and Mackenzie Calhoun show up in the TNG book, Before Dishonor. However, it can really only be considered a cameo appearance. Calhoun and co. show up for the ending and fight along side Picard and the Enterprise, and Calhoun chats with Picard at Janeway's memorial. But still...that ties in the NF crew with the TNG era trek-lit, quite nicely

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