My favorite is Lightning/Francesco: "You should try taking your fenders off, you'll like it!" Even in a non-slash context, I love the way those two managed something resembling a friendship by the end of the movie.
Mater/Otis: I'm not sure if I can see them romantically involved, but I love the close friendship they share.
Tomber/Finn, just because.
I expected to find slash potential between my favorite characters, Grem and Acer, but I couldn't really see it. Not that I wouldn't eagerly read anything anyone comes up with for them, but I'm more intrigued by their sorta-friendship, which is apparently unusual among Lemons who hate each other.