Shinjuku Sakaba Genki Kaifukudou
Genki Kaifukudou is an incredibly cheap izakaya in Shinjuku. Beer and a lot of dishes are only 290 yen, so it's a great place to fill up on booze and food if you blew your budget the day before. It's a good place to come with friends, for gatherings or office parties.
There are Isomaru Suisan restos almost everywhere in Tokyo. What's great is that they're open 24/7. They specialize in "hamayaki", which is basically seafood BBQ. You get a small BBQ grill at each table to grill all types of different seafood and fish. The fish is fresh and of good quality, and it's good! They also have nice lunch specials.
Miyazaki Prefecture Nichinan Tsukada Farm
This restaurant offers great food at a reasonable price. They also have a nice sake selection. It's a great place to come with friends or even with your family. The service is really friendly and welcoming. Don't worry if you don't speak Japanese as they have an English menu too.
Tofuro has a really cool interior and is great for large groups, or even for smaller groups as you can get a private room. They have quite an extensive menu, and it's great for sharing. You can get all sorts of Japanese cuisines, such as sashimi, yakitori, etc. It's also affordable.
Imaiya is a casual izakaya in Shinjuku with a cool interior. This resto specializes in "yakitori" (skewered grilled chicken). Each individual brochette is a little pricey, so you might be better off with the course, it starts at 4,500 yen and you get 13 different dishes (more for the pricier courses).
Torigen is a reasonably priced izakaya, which also specializes in yakitori. It's a great place to come with a few friends to share a few beers and eat nice meat and vegetable skewers. You can order piece by piece or as a set meal depending on your hunger level.
Ika No Sumi Shinjuku
"Ikanosumi" (which means squid ink) is a really cool izakaya that serves beautiful seafood in Shinjuku. It's a great place to have fish sashimi and also sake. You can reserve a long table and come as a large group, or with a few friends and you can get a private room.
This is another resto open 24/7 and it has a very cool interior. As you may have guessed from the name, they specialize in gyoza. They serve all types of gyoza: grilled, boiled, in a soup, deep fried, etc. They also have nice sets, such as gyoza, beer, and edamame. It's a great place to have a drink and snacks with friends, before or after going out.
Kichiri feels like a more upscale izakaya because of it elegant and modern interior, but it's actually affordable! In fact, they have a very popular roast beef course, which includes an all-you-can-drink course, for 4,500 yen. It comes with roast beef of course, and also tofu, salad, fried potatoes, mentaiko udon, etc.
Hibiki is a beautiful izakaya located on the 49th floor of the Nomura building in Shinjuku. Compared to other izakayas in the area, it's rather upscale, but it still has a convivial atmosphere, where it's pleasant to share dishes among friends. The dishes are simple, yet delicious. For example, the soft tofu is served with only soy sauce and sea salt, yet it's sublime. The steak is great too! It's grilled and served with ginger and miso...it's melt in your mouth goodness.