The Runaway Bride. The Doctor asks Donna if she's human, she asks "is that optional?" He responds "it is for me."When did RTD ever mention the Doctor being half-human in a vague sorta way?
There's also a scripted bit from TEOT which wasn't filmed, but is included in The Writer's Tale. Cactus Lady decides to review the facts with the Doctor. Exchange goes something like this:
Cactus Lady: So, let's see if I understand everything. Mr. Saxon isn't human?
Doctor: No.
Cactus Lady: Right. You aren't human either?
Doctor: No. Well, I was briefly. New Year's Eve, 1999. But I got over it, like the flu.
The reason RTD removed it is he felt it would confuse fans of the modern series who weren't familiar with the 96 movie and would be distracted thinking "but Human Nature didn't take place in 1999."