Somewhere on JF I think masaegu or another native Japanese speaker posted a link to a publishing guide or university site or something identifying broad categories of words for which kana is preferred. I can't find the bookmark offhand.
In the meantime, for whatever it's worth, Wikipedia-JA has a guide for their preferred style of writing:
Wikipedia:表記ガイド - Wikipedia
It includes their adopted conventions for kanji usage. You might check it out for a little instruction (although their conventions don't match up with Japanese newspaper conventions perfectly).