Blue Grotto in Brookside is great for pizza, if you're into that.
West Side Local might be my favorite restaurant in the city. I know the person that grows the vegetables they use, which makes it that much better to me.
La bodega is pretty great (the original, not the one in Leawood)
Room 39 has a great (the best) brunch. Again, not the one in Leawood.
edited to include:
Bluestem, should go without saying.
Potpie (right next to bluestem) it is delicious, try it.
and, R bar in the west bottoms. best drinks in the city, and probably one of the best menus also.