Menya Kissou, due to its overwhelming popularity, has the longest line I have waited on in a long time. It was at least 45 minutes, with several winding turns and then seats, in 30+ degree heat on an August Saturday afternoon, after a 10-15 walk from Kiba Station on the Tokyo Metro Tozai line. If you take the Suplek's database as your gospel, then Menya Kissou is the answer to the question I get a lot: "What's the best ramen shop in Tokyo?". There's an Oshinagaki on the wall with their simple menu, and two people working feverishly in the shop. Only one choice of broth, a standard lightly-colored tonkotsu gyoukai, a ligher and cleaner and saltier taste than a place like Tetsu. The noodles were on the thin side, and the chashu was the cut cold type. All very good. The place is only open 3-4 hours per day and the two workers were friendly but talked very little. There's a drink machine at the beginning of the line near the shop on the corner, that's how far the line stretched. Bring one of those little chairs you can get at the discount shop for 500 yen. All I can say is that the tsukemen was very good, but personally I don't think it is the best in Tokyo - and it wasn't worth waiting on line 45 minutes for. I won't argue with Supleks or Tabelog's ratings since they reflect what the general population of Tokyo likes, but I can say that while it is "Recommended" (if the line is < 15 people long or so), and it is extremely good, it's not my #1.
Supleks page where you can see the ranking
Diddlefinger Map (English labels)