I would consider linking characters by various criteria (the sound, the radicals, the meaning). In Chinese my experience has been that understanding the relationship between characters is not a science. What I mean is, I don't really care if you are giving me the perfect ancient etymology of a word or character so long as I am able to explore and relate characters in a way that makes sense to me.

Yeah, definitely devin. What we'd like to do is create both a character decomposition system and a mnemonics system that would be seeded across users so that people can get the stories (and hopefully by association) the character lodged in memory. A lot of Chinese-English dictionaries have exactly this sort of organization.