On page 126 of 333 of the iBooks version, half-Vulcan/half-Romulan character Soleta is introduced to none other than the Doctor from the TV series Star Trek: Voyager but she abruptly compares him to some untold previous meeting with the Tenth Doctor:
Soleta looked momentarily confused. "The Doctor? I met a man called the Doctor once. Wore a long brown coat and a blue suit. Very odd person. This isn't him."
On page 289, the Doctor has just uploaded a virus designed to remove the out-of-control artificial intelligence calling itself Morgan Primus from the starship Excalibur's computer systems and resets one of the Tenth Doctor's repeated catch phrases:
"It has already wormed its way into your core programming, and requires a simple phrase, spoken by me, to activate it. And that phrase is," said the Doctor, and there was great sadness in his eyes, "I'm sorry. I'm so sorry."
And on page 292, there's what appears to be a possible nod to the Tenth Doctor episode "Blink" as the dying Morgan Primus has a final conversation with her daughter Robin Lefler:
And Morgan looked in the direction of her voice, and she reached up and caressed Robin's face. "Don't look away...from Cwansi...don't blink....if you blink...he grows up..."
There may be other shout-outs in the novel somewhere, but these are what I caught my first time through. Since Peter David is an admitted Doctor Who fan, here's hoping these aren't the last of his shout-outs to the series or the last of his wonderful Star Trek: New Frontier novels. If nothing else, I would love to know what exactly happened when Soleta met the Tenth Doctor, wouldn't you?