Seto Kaiba
His older brother, Mokuba cares about Seto more than anyone in the world. The two are almost inseperable - Aside from when Noa decided to use Mokuba as a shield, of course.
Noa Kaiba
Noa originally kidnapped Mokuba so he could use him against Seto. Towards the end of the series, he and Mokuba develop a friendship- Mokuba hopes to see him again someday.
Yuugi Mutou
Mokuba considers Yuugi as a friend rather than a rival - Unlike Seto. Yuugi is often the first person he turns to when Seto is not an option.