There are a few words, which are written with Kanji imported from China, but where the intended native Japanese meaning would prefer a different choice of Kanji. My favourite examples are
雷 vs. 神鳴り (cf. 海鳴り)
鶏 vs. 庭鳥
向日葵 vs. 日回り
Does there already exist a list of these words? If not, can anybody come up with more examples?