I went to a really great new wine bar in Nishiazabu called Parabola (see http://www.thedevilinthegrape.com/) which opened a few weeks ago. One of the partners in the bar, Julian Stevens, used to work for Berry Brothers (oldest UK wine merchant) and has a fantastic taste in wine, which is reflected in the selection.
The wine bar has a very large number of wines, but for each day they put out a 2 page menu which contains a selection of those wines. I was told that in most cases, they only buy a dozen or so bottles of each wine, so each wine runs out pretty quickly, which means that much of the menu changes every day.
There are some fantastically well-chosen wines - it is a real wine lover's place. You won't find massive, blockbuster Napa oak monsters (urrrgh) which are sadly so popular these days. Instead the wines are very well made, elegant offerings from around the world. Very humane prices as well, plus what must be Tokyo's biggest cheese platter.
The place has only just started off so the people running it are what I would consider unsually flexible and generous. Hopefully that will last even after the place becomes better known, but if you like wine it is a good idea to go and pay a visit now. They are open every day except on Mondays, and one of the people running it told me that they only close when the last customer leaves (which apparently has so far varied between 3 am and 6 am).
Definitely worth a visit (though it is dangerously close to my home, which means I have been 3 times in very quick succession and am the worse for wear today).