The first place that comes to my mind is Tsuki at 1441 W. Fullerton. 773-883-8722. They have really put together a thougthful wine list there with the specific intent to match wines with the cuisine. Too many Japanese restaurants just let their liquor supplier create a wine list for them, filling it up with wines that are on their agenda, and not really matching them with the food.
Besides having a good wine list, Tsuki has excellent food.
"Dis-moi ce que tu manges, je te dirai ce que tu es."
~ Brillat-Savarin ~