Mega Man Volnutt and Roll Caskett's relationship, really, whether you choose to take it as romantic, friendship, or familial. They're very comfortable around each other, their banter is light-hearted and warm, and if you're very nice to Roll during Megaman Legends 2, she writes in her diary about how wonderful Megaman is and that she loves him. Also, there's a moment in Megaman Legends 2 where Tron tries to break up Megaman and Roll by using a voice-changer pretending to be Roll (and locking Roll out of her connection so the real Roll can't interfere). Tron then proceeds to tell Megaman all kinds of crazy lies in Roll's voice, such as that she never really cared about him, she skimmed profits off the top at his expense, she thinks he's an idiot, etc. It almost works, but after Megaman beats Tron, the real Roll manages to chime in and Megaman realizes Roll would never really say those awful things (though Megaman doesn't actually tell Roll what Tron said in her fake Roll voice), and they have some cute banter about milk.
The second game confirms that, at least on Roll's side, it's definitely romantic. If you're nice to her throughout the game, her final diary entry her her write down that she does love Volnutt, but has no idea how to tell him.
In the first Megaman Legends game, Tron's slow realization that what she's feeling about Megaman is love. At first it starts as her wanting him as a useful servant, then she doesn't get angry after Megaman beats the Bonnes and wonders why, then she notices she has a strange feeling about him, and then she realizes she's in love with him. The whole development is presented as a young girl feeling "womanly feelings" for the first time, and it's heartwarming to watch. More heartwarming since this is a villainess going through this development.
In the first game, after you defeat the Bonnes' Fokkerwolf, Tron tearfully apologizes to Teisel for losing as their ship goes down in flames. But instead of shouting or getting angry, Teisel calmly tells Tron that she tried her best, and that sometimes even though their best isn't good enough, that's just the way life is and there's no shame in that. It shows that even though they're the villains, they're still a family that cares for each other. Watch it here.
Not long after, Megaman stumbles onto a giant robot, and notices a familiar emblem. At that point, Tron shows up...and he is absolutely overjoyed to learn that they survived the crash, in spite of everything they put him through. Tron's reaction to this was the icing on the cake.
In the first game, Ira, a young girl who is hospitalized for a leg injury. Upon talking with the hospital staff, and making a small donation, Mega Man can purchase new equipment for the hospital, resulting in Ira recovering a lot faster. When you see her next, she will run up to you, expressing gratitude for helping her walk again. Aww.