Non-romantic:

Sigma and Phi from Virtue's Last Reward



Heather and Douglas from Silent Hill 3



Bowser and "Chippy" from Bowser's Inside Story



Riku and Mickey from Kingdom Hearts



Female protagonist and Junpei from Persona 3



Romantic:

Fran and Balthier from FFXII



Fei and Elly from Xenogears



Shulk and Fiora from Xenoblade Chronicles



Kanji and Naoto from Persona 4