"Service charge" is most often found in hotel restaurants. Some other touristy places that can get away with it (like TGI Friday's, Hard Rock Cafe, etc.) will also charge a service charge after 5pm.

Several years ago, a law was passed stating that all prices had to listed inclusive of tax. So if you see a food item listed as 500 yen, the food itself costs 477 yen, with the 5% tax (23 yen) baked in.