The Doctor first encountered Captain Archer's "temporal cold war" and identified T'Pol as a "Preserver" agent like Gary Seven in By His Loose Laces.
The story of the Doctor's father is told in the trilogy comprising Transformations, One Child Born, and Posterity; with allusions throughout other works.
The Doctor was revealed to be Merlin in the DOCTOR WHO serial Battlefield. (There being a time anomaly involved, he was as surprised as anyone.)
The first part of the trilogy of the Doctor's redemption of the Chosen Jedi is Episode VII: The Battle for Coruscant.
Starfleet (specifically Captain Picard) learned of the Doctor's connection to Romulans and of the Tradition of Dorek in Sela.
In Everything in Threes the Doctor told Picard no vampires survived the post-atomic horror. In For To Carry Me Home the Doctor met Angel on Archer's Enterprise.
The Master attempted to parlay capturing the Enterprise into capturing the Federation and the Klingon and Romulan Empires in Under Seige.
The eugenics data used by Wilson's service was procured by Kirk in The Secret of Siphis.
The flashback to the meeting between the Doctor and Rassilon in the Doctor's past and Wilson's future is to events of Historical Revision, my first full-length DOCTOR WHO/STAR TREK crossover.
The Doctor enlisted Kassidy Yates' assistance to contact Captain Sisko previously, and assisted the Voyager EMH in initiating the hologam civil rights revolution, in In Thy Image.
The Doctor previously visited the tomb of Rassilon in the twentieth-anniversary DOCTOR WHO serial The Five Doctors.