As I said above, some parts of Logan's 2nd half eerily reminded of X-Men Origins: Wolverine.
1. In Logan, Transigen creates the perfect killing machine Wolverine X-24. Origins had that genetically-mutated Swiss-knife Deadpool freak, Weapon XI.
2. Logan meets Eriq La Salle and family, invited to their house and they end up being killed. Origins had the Hudsons who took in Wolverine to their farm and end up being killed by the bad guys.
3. Transigen is hunting down mutant kids and they end up escaping at the end. Origins had the bad guys capturing mutant kids and they end up escaping at the end.
Though Logan is not based on Old Man Logan comic book (not even loosely based), there is still a quasi homage to it when it's revealed that Professor X, not Wolverine, killed the X-Men when he suffered one of his seizures.
It's strongly hinted that Charles did something awful to the X-Men and fans will be slowly dreading the reveal during the first hour. But when it's finally revealed that Charles killed them and he finally knows what he did for the first time, that scene was just heartbreaking.
I'll add more later when I have the time.