While there are a multitude of relationships I could cover, this page will mainly focus on two characters combined: namely, Akihiko Sanada and Shinjiro Aragaki.
Akihiko is probably one of the first friends Mitsuru ever made, even if it was namely for business regarding SEES. The two were the only members for a time, and as such had a sort of bond that wasn't present with newer members like Yukari. They have a business relationship mainly, but also care for each other very deeply as friends, even if they don't show it. Mitsuru is overly critical of Akihiko and his 'act first think later' personality, which usually lands him in trouble with her. It's not something born out of distain or spite though--it's more out of concern of worry, because goddammit Akihiko you're gonna get hurt again.
While there isn't much of a relationship between Mitsuru and Shinjiro, she is aware of who he is and what he means to Akihiko. She is aware of the events of Akihiko's past and his looming self-hatred because of his inability to save his sister. Which really nails the fact that Akihiko and Mitsuru are more than just business partners--they're friends, as well as comrades.
Mitsuru's relationship with Shinjiro is complex--they respect each other, but don't have much of a relationship, if any. Which doesn't stand for much considering Shinjiro isn't really friends with anyone and tries his goddamn hardest to keep Akihiko at bay. The relationship between the three of them however, is dynamic. They all act like childhood friends despite being so, purely based on their individual respects for each other. When Shinjiro either dies or is knocked into a coma, it hits Mitsuru hard. Though not as hard as Akihiko, she still feels a deep impact.
If you'd like to learn more about Mitsuru's relationship with Yukari, please visit my shrine to the two of them, entitled Angels.