Table Top Cooking:
Nabe (stew), Okonomiyaki (Japanese pancakes), Sukiyaki and Shabu-shabu (hot pot), and Yakiniku (grilled meat) are quite popular in Japan. It's great when having a big group of people over, or if mom needs a break from cooking; everyone cooks their own food on a hot plate/griddle/grill in the middle of the dinner table.
Kushi-katsu (deep fried foods):
Meats and vegetables are first dipped in batter, rolled in panko bread crumbs, then deep-fried. Pork cutlets (tonkatsu), chicken cutlets, korokke (croquettes), and various other foods are cooked in this way. There are many Kushi-katsu restaurants in Japan where you can choose your own foods, then deep-fry them yourself at your table. Shrimp or fish can be cooked this way too. If you leave out the bread crumbs and just use batter, this is called 'tempura'.
Stir-fried vegetables (self-explanatory)
Yakitori (skewered chicken). You won't find just the breast meat, but also chicken meatballs, chicken skin and chicken hearts on a skewer.
Ordinary deep-fried foods like karaage (chicken pieces flavored with ginger, garlic, soy sauce, then breaded and fried), abura-age (deep-fried tofu), harumaki (egg rolls), ika (squid) and tako (octopus) are pretty popular.
The kim-chi flavor (in stews and the pickled vegetables themselves) is quite popular, having been borrowed from Korean culture.
The teriyaki flavoring (sugar, rice wine, rice vingear, soy sauce, water) is VERY widely used.
Sushi, onigiri, musubi (a variety of meats, seafood, vegetables combined with rice and wrapped in seaweed).