Thomas Wayne is the son of Bruce Wayne and Natalya Trusevich in Detective Comics vol. 2 #27, in the story "The Sacrifice."
The Phantom Stranger shows Batman a vision of an alternate life, where his parents were never murdered. Bruce has a family with his parents, his wife Natalya, and his son Thomas. However, Gotham City is overrun by crime, Ra's al Ghul has conquered a quarter of Europe, and Dick Grayson is on Death Row. Batman sadly chooses to return to his own reality.