Having been rereading all the Marco books and Visser for working on fic, I really love Eva and Peter. Eva's smart, resilient and self-sacrificing; Peter's emotional, flakey and nerdy. I can totally picture how their relationship went and what troubles they might have run into, what things they had in common.
As for less-minor characters, Erek. I love that the resident pacifist manipulates a bunch of teenagers into murdering a race of children. He's self-righteous, crafty, manipulative, at times passive aggressive, and yet he's one of our good guys. I love that.
And of course, Edriss 562 is incredible.