For myself, I collected little statues from each place I went in Japan. They are small, durable, and uniquely Japanese. I have everything from Buddhas to Geishas to the 7 Lucky Gods to Neo and oni. I also have a few black velvet hanging wall scrolls!
For omiyage, I'd buy local food that could be shared.
For family, I bought silk yukatas and some nice little items, like a lacquered jewelry box and fans.