I watched There Will Be Blood about a month ago, and while your description is overly brief and seems to give the impression that he never sees his son again until the son is a man(not true, the son actually returns after a year or so, having learned sign language), I never saw it as a father-son movie. If anything his rant to his son when th son mentions opening a business of his own is the best summary of the movie. Here is an oil tycoon who hates losing, hates competition, and he will use and do whatever it takes to make sure he's not just the one on top, but the only one within miles of the pyramid.
to my (admittedly somewhat aged) mind you're missing The Champ (1979)
you can pretty much guess the core reason why from that single pic...
that film is completely infamous in my country/local/generation for turning even the hardest of men into blubbering wreaks...i know more than a few people who've been hunted just for asking about it of such men after they've said something "real men don't cry" or some suchlike :P
"but...what about The Champ ?..."
"you can fuck off !"
I remember really enjoying Frequency when I saw it years ago, it's pretty clever and has an emotional core. It seems like nobody really talks about it or mentions it's existence.
The technical aspects of it's timeline altering premise don't really make that much sense, but it's not trying to be Primer.
Dunno if it's cuz I have no father but those movies don't make me cry in fact you never listed a movie that made me cry.
Fun list tho