Thanks to all the 'hounds that provided recommendations for my Asia swing (lamentably, the info on Beijing and Seoul is pretty light on this board, but Tokyo was right on).
Had two great meals (three actually, if you count a fun DIY grilling experience in one of the MyCity department store restaurants in Shinjuku).
For those looking for raw fish, the first was at Ginza Kyubei (7-6, Ginza 8-chome, Chuo-ku, Phone: 03-3571-6523). Small joint -- there's a bar downstairs where it's a ratio of one chef to 1-2 parties with about 15 total people dining at any one time, with some private rooms upstairs. On one of those Ginza back streets. English friendly (although everyone else eating when we were there was Japanese, so definitely not a tourist place). The tab for three people was $500, but well worth it -- extraordinarily fresh and inventive preparations (a handful of rock shrimp were dispatched before our ears and were ingested moments later).
For kaiseki, we went to Takamura (3-4-27 Roppongi, Minato-ku, Phone: 3585-6600). In my visits to Kyoto, had sampled some excellent kaiseki and this ranks with the best. It's amazingly a Japanese country home nestled amidst the trees on a hill in Roppongi (yes, I know that sounds odd given Tokyo's density, but true). Must reserve far in advance and there's a minimum of four in a party, as you dine in one of 7-8 private rooms. About $800 for a party of three, but quite memorable. Again, amazingly English friendly, and as artful as kaiseki can be. We also ordered some Kobe beef (which was personally grilled by a chef in the corner of our room) -- definitely a different experience than the Wagyu beef you get stateside.