My local French place charges 300 yen cover but that includes a delightful amuse bouche where they marry Japanese ingredients with a French touch. There is no service charge. I think 300-600 yen is common for nicer restaurants and better izakaya. And it's often time dependent like after 6 pm.

I think some of these hole in the wall bars charge maybe 800-1000 yen cover but it includes a drink. This hilarious Yngve Malmsteen themed bar in Shibuya across from Bunkamura (I actually recommend checking it out) charges 1000 yen. It's too bad because if I could drop by and have a drink for 600 yen (what they charge) then I might be convinced to drop by more often since I walk by it nearly every day.

http://malmsteen.jp/index.html