OK, it's not fair to call all this stuff 'junk'. I love it, all of it. But where else to put it? Others do a better job than me of finding this stuff, but if you need a few pointers, these won't steer you wrong. Most of are within striking distance of my home or office, but that too is a cross we have to bear if we want recommendations, right? You should be able to find something good anywhere in these categories.
Try something like RamenTokyo for a serious view on this, or Ramenate, back when he was cool (i.e., living in Tokyo). I only started being more serious about ramen-eating around April 2010. Until then it was all miso ramen with me; now I almost never eat that, and don't have any good ideas on where to get it (I tell a lie, Junren is famous even if I didn't like it).
After getting over my miso ramen fascination, it was straight into pork bones...and that hasn't stopped yet.
Kissou, Kiba You can hate on it for being too popular, but I've never again had ramen where every item was so individually good. Then again, I didn't know much at the time. Expect to wait a lot.
Tsujita, Awajicho Very good version of the soup style and tsukemen concept from Kissou and lots of others circa 2008. Expect to wait a little. The nearby miso version is also awesome (I really did tell a lie above, didn't I?).
Ikaruga, Kudanshita The garlicky maze-soba with chunks of pork are insane. Expect to wait a little.
Takatora, Takadanobaba Balanced pork-fish soup with big chunks of pork and great noodles? I'm on that any day.
Kandaya, Kanda Seems odd to call this 'Yokohama style' ramen since it's so pork-bone focused, but it's a lip-smackingly good bowl of noodles. More straightforward than most of the modern, niche-y ones above.
I love this stuff and have been to a lot of places, but most don't measure up even close to...
Hakata Furyu, Kanda Straightforward Hakata ramen (light, fatty pork soup; thin, straight, tough noodles) but somehow it makes me go back. Many times. Spicy pickles, garlic, ginger...it's like the breath of a god. And dead cheap at Y500, free refills. Branch right under JR 'Baba tracks near Takatora.
Ippudo, Roppongi My colleague tells me the best ramen he had in his life was at Ippudo's original store in Fukuoka, and that the Roppongi branch sucks. If it sucks, I don't think I could handle the honten. On the other hand, I haven't been for years (so no post), and I may have grown up ramen taste-wise. The lunch set mini-gyoza with yuzu kosho paste are great too.
Not all that precisely, I'm defining this as 'brown translucent soup with medium, lightly-curly noodles'.
Ganko, Waseda For connoisseurs, the subtle differences and deep flavor of this bowl are likely to be a real find. For other people, they'll just feel cool that they found the unmarked storefront in the alley, hidden by a ratty black tarp.
Bigakuya, Toyocho When I ate this, I thought "So that's what old-fashioned ramen is supposed to taste like." Since then I've been trying to find a peer, but no one comes close.
Fukumen, Jinbocho What style is this? A really strong, deeply-flavored clear-but-meaty soup with strong, curly, yellow noodles, huge piles of bean sprouts, and thin slices of fatty, soft, delicious pork? Whatever style it is, it's the style that makes me go back all the time.
Kikanbou, Kanda Under and among the dramatic quantities of red chili and prickly ash pepper are delicious tonkotsu soup, excellent noodles, and awesome pork. Gives me the shakes just thinking about how my mouth (and stomach) felt afterward.
BeerA lot of people would say beer isn't a food, and that it should come at the bottom of the page, after the foods. To them I say "Piss off, suckazzzzz! Get me another damn beer!"
Ushitora, Shimo Kitazawa I feel a bit like I'm being untrue to Popeye, which is practically in my neighborhood, but the fact remains that these guys have all the great microbrew that you could want to drink plus decent food.
Popeye, Ryogoku On beer-only grounds, this is probably the winner. Go before 8 (I think) when 'happy hour' means you can get some of the crappy food free with every beer. Note that it's basically micro-brew in all its forms; I think they have bottles and Belgians too, but for that you should go to
Houblon, Ginza 300 varieties? Can't go wrong. Except with the sucky, sucky food.
Delerium Reserve, Akasaka has great Belgians and good food. Belg Aube in Roppongi is a sister store (and they're all associated with the famous brewery, so expect goodness on tap).
Favori, Ginza Fewer varieties, better food, quirky self-service system, I like it. I know I went there in 2009, but for some reason didn't blog it. Must have assumed I had already gotten that done on a prior visit.
I have not been to Butagumi or Tonki; I don't like to travel for junk food. Except beer, which we already established is food.
Yamaichi, Awajicho I don't really see how this could be bettered. I even went back to confirm and was just as stunned as the first time - which is no mean feat. Note that Katsuman is just around the corner (if facing Yamaichi, go to your left, then first right) and 95% of the flavor.
Katsukura, various in Tokyo, Kyoto and others. If you couldn't go to Awajicho, this is the chain that I'd recommend. I haven't visited one in the blogging years; the one in Roppongi Hillz clozed. We used to go there a LOT.
Kameido Gyoza, Kameido If you say 'gyoza', this is all I want to talk about.
A weird category, and one that I mostly eat when I want something easy and comforting.
Bistro Bonnes Mares, Kanda is the only place I'd really recommend - the depth of flavor in the sauce is uncanny, and I've had it multiple times.
Beer Chimney, Marunouchi is where I go to overeat on shitty-quality yoshoku when I'm having a bad day at the office. I don't really think you should go.
...is at the bottom because I don't care so much. There must be better places all over the city, but I haven't run into them accidentally. Near the office(s), you should try:
Muromachi Sunaba, Kanda More old-fashioned refinement and grace than nearby Yabu, great noodles, and definitely shorter lines.
Honmura An, Roppongi This rec goes back a few years, but I think it exemplifies some of the modern 'soba dining' ideas.