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In "The Night of the Doctor", the Eighth Doctor mentioned the names of several of companions who originated in the audios. That was the first such reference to non-TV companions. Several non-TV stories have also been adapted for the TV show -- extensively adapted, changing the incarnation of the Doctor, the enemies, the plot, &c.

Additionally, there have been subtle references, such as the reference the Cybermen originating on Marinus in "World Enough and Time", a reference to "The World Shapers" (comic story), the events of "The Monsters Inside" (novel) being referenced in "Boom Town", and the Doctor mentioning being to the frost fair 'several times' in "Thin Ice" (only one of which was on TV), among others.