On Sunday night, I went with a group of people from my sake class to A-Isshin, an izakaya near Shinjuku san-chome. This was the second time I'd been there, although the first time I'd actually eaten (my first trip there was right after the soba pilgrimage I've previously written about--no more food was possible).
The great attraction about this place is the huge range of sake they carry, and the knowledge of the master. There seem to be three main methods of ordering your drink here: 1) off the menu (but given that only the brewery name is written, this is a bit of a hit-or-miss proposition); 2) stand in front of the huge sake fridges and pick something, or; 3) pull the "I'd like something like this..." and see what the master comes up with. The groups' two favorite sakes of the night-one called Mansaku no Hana, one called Tamahagane, both daiginjos-came through this method, and it's what I'd recommend doing.
The menu is fairly standard--sashimi and the like, with a bunch of large dishes out on the counter, and a variety of nabe (hot pot) types that aren't written on the menu but seem to be generally available. I've only been in one of the back rooms, but this seems like it would be a good place to drink and nibble on things at the counter.
You get a bit of the master's life philosophy hand-written on the chopstick wrappers. I particularly liked the one I got the first time: "People ask me why I don't carry (insert name of famous sake brands here). I tell them it's because they don't taste good. Reputation and flavor are different things."
My main quibbles with the place: the sake menu is hand-written in a particularly flowery script that I have trouble reading, and no prices are given for the sake. I recommend bringing along a native Japanese speaker/reader, and asking for prices if you're on a budget. Our evening ended up at Y10,000 per head, probably less than half of which was food costs.
5-17-5 Shinjuku, B1