Iris calls Drayden grandpa in gen 5 games iirc tho I dont think they're biologically related

Gen Fu from Dead Or Alive

Grandfather Ghondor from Xenoblade 3 Future Redeemed

crap i misread ur title, dont think ill be able to give any sadly :(

Kronos from God of War 1 & God of War 3 is Krato's grandfather. Kratos doesn't lovingly refer to him as grandfather, but the relations still there. Chaos from Hades is technically Thanatos' and Hypnos' grandfather, though their non-binary nature means it's down to you whether they are both a grandmother and a grandfather, or whether they are neither. Grampa Simpson appears in a few of the Simpson games like Hit & Run and Simpsons Skateboarding. Professor from Ape Escape 1 is Natalie's/Natsumi's/Katie's (localisation amarite) grandfather. I'm sure someone in one of the Mortal Kombat games is a grandfather to another character, I just don't know it well enough. Idk if Sparda appears in any of the games Nero is also in from the Devil May Cry series, cause then ig that'd be added lol. The Grandad from Rugrats appears a few times in Search for Reptar. JoJo's Bizzare Adventure: Eyes of Heaven has nearly every main character from all then-published volumes of JJBA, and since they're nearly all related, there's going to be a few people who are grandfathers to others (Jonathan is grandfather to Joseph, Joseph is grandfather to Jotaro). I think they see Largo Potter from Valkyria Chronicles 1 as the grandpa of the squad, though I can't remember if they actively refer to him as such. Sorry for the massive text dump, hope this helps.

Gaulf from FF5, Strago from FF6 and Cid from FF4 The After Years