The Doctor's children included thirteen children with his wife "Patience". Susan Foreman's father was the eldest of these children. (PROSE: Cold Fusion).
Miranda Dawkins was the daughter of the Emperor, a future incarnation of the Doctor, who was later adopted by the Eighth Doctor. (PROSE: Father Time)
The Ninth Doctor related to Dr. Constantine's remark about having been a father and grandfather in the past, claiming "I know the feeling". (TV: The Empty Child)
The Tenth Doctor commented to Rose Tyler that he "was a dad once". (TV Fear Her) Later Jenny was the daughter of the Tenth Doctor who was artificially created from his DNA by a progenation machine. The Doctor mentioned to Donna Noble that "I've been a father before, lost all that a long time ago" (TV: The Doctor's Daughter).
Amy Pond once asked the Eleventh Doctor if he was a parent, he did not answer (TV: The Beast Below). At Demon's Run Amy again asked the Doctor if he had children, he replied "No". Amy then asked "Have you ever had children?" He did not answer.
The Sapling was a sapling of the Planting who was infused with some of the memories of the Eleventh Doctor and Alice Obiefune as his "progenitors". (COMIC: The Scream, et al)