Anyone that has ever been to an anime fanfic site knows that lime refers to intimate situations that are implied but not shown. Actually, it goes a bit further, it doesn't just mean intimate, it means sexual. Whatever. At the core, love and sex, while not necesarilly the same, run just as deep. And if lime refers to subtle but definite hints of intimacy, be it physical or also emotional, then To-ya and Yuki's relationship is as limey as they come. Throughout the series there are constant details that indicate that the nature of the bond between the boys goes far deeper than platonic friendship.
Hint of Lime deals with that elusive but quite obvious bond, with the little and not so little things that give us insight into its nature, and with what they might all point to.