Campanella and Giovanni from Night on the Galactic Railroad. For those who think I'm a yaoi fangirl through and through for shipping these two, come off it. I try to ship at least one thing for everything I'm a fan of. It's a force of habit, whether it be two males, a male and a female, or two females. I try to analyze any relationship possibilities between characters, and even if there is none, I'll still attempt to ship it. Doesn't mean I believe it'll happen; just means I think it's cute.
Campanella and Giovanni seems like it would be the only plausible couple, unless you are full of hetero. Then you could ship one of them with the girl they meet for a few minutes. But other than that, these two have the only 'deep' relationship in the book and film.