Sort of, yeah. But you're not playing as the parent, but as the child.

I was about to say that.

Anyway, Booker DeWitt from Bioshock Infinite surely has to be on the list.

It was more of an implication, really, but the PR materials for Dishonored 2 outright tell you that Corvo is Emily's father.

Assassin's Creed 3 (m/b others; don't remember, don't care)
Castlevania - several games' protag sired future protags
Kane and Lynch 1&2
Lost Odyssey
Manhunt :(
Marvel Ultimate Alliance - several characters
Metal Gear Solid 3 (m/b others, grew tired of the franchise)
Metro: Last Light
Okami
(?) Postal 2 - did Postal Dude have a child? I know he had a wife/girlfriend and a dog. I don't remember.
The Punisher :(
X-Men Legends 1&2 - a few characters

God I hope not! :P

Right, but I seem to remember a kid crying while his wife/gf/whatever was talking to him at the beginning. Not to say it would even be his own child if I haven't just misremembered the whole scene (very possible).

In one or two of the 3DS Fire Emblem games you not only have a child, but the first part with the parent is basically the prologue or just the beginning, as you have a timeskip and play as the child, which is the main portion of the game and they're the 'real' main protagonist.

Same thing happens with all Rune Factory games, unless I'm mistaken. At least most or all the DS RF games have it.

Fallout 2: not directly 'in-game', but you're the grandson of the dweller from F1 and if you take some paths, you can have a child in New Reno, but you will never 'encounter' him/her.

Has Stardew Valley been mentioned? It's of course optional but you can.

Yup, it's the first game I mentioned.
It's interesting that the option is available even if your character and his/her loved one are of the same gender.
I can't think of many games that allow this.

I don't remember this. Is it related to the mob quests in that town?

I would say Bent Svensson, one of the protagonoists in the Adventure game <span class="bold">A New Beginning</span>, has also a son. The son is a non playable character in the game and part of the story.

FEAR 2! Michael gets a child with that super cute little girl Alma!

*envies* *envies*

Yes, specifically to the Bishop family.

That's actually quite interesting. Thanks for the info!