Tokyo has thousands of bars with great music and atmosphere, romantic views and interesting people. Here are a few that have also distinguished themselves with their impressive drinks selections.
Legend:

A good, comfortable place to get started.

An encyclopedic menu, with the best selection in town.

More a restaurant than a bar, but with a good drinks list.
Scotch whisky
Helmsdale (Nishi-Azabu). 300 single-malt whiskies (up to Y10,000 a shot),
till 8am; they even serve haggis! 03-3486-4220. Minami-Aoyama 7-13-12.
HazelBurn (Kabukicho). An impressive line-up of Scotch whiskies and Scottish-style
food. 03-5285-1470. Kabukicho 1-6-6, Hashimoto Bldg. B1F.
Speyside Way (Jiyugaoka). Over 800 kinds of whiskey at this specialty bar.
03-3723-7807. Jiyugaoka 1-26-9, Mikasa Bldg. 5F.
George's Bar (Kichijoji). A traditional cocktail bar with good martinis
as well as a respectable Scotch selection. 0422-22-8002. Kichijoji Honcho 2-19-7.
Tequila
El Paso (Omotesando). Filling Tex-Mex food and a big tequila selection. 03-3479-1995.
Kita-Aoyama 3-5-17.
Agave (Roppongi). Hundreds of tequilas, served in a cave-like basement
bar. 03-3497-0229. Roppongi 7-15-10, Clover Bldg. B1F.
Grappa

Esperia (Nishi-Azabu). There are usually a few dozen after-dinner grappas
available, and more if the staff has just come back from Italy. Great food, with
lots of interesting cheese dishes. 03-5485-1771. Nishi-Azabu 4-11-25.
Aquavit

Stockholm (Akasaka). 8 different aquavits and a good Swedish smorgasbord.
03-3509-1677. Nagatacho 2-14-3, Akasaka Tokyu Plaza 1F.
Schnapps
Kandagasse (Akihabara). 9 types of German schnapps, plus good beer and
food. Accordion alert: live music Thu-Sat nights. 03-3254-1339. Soto-Kanda 2-4-4
B1F.
Sake
Akaoni (Sangenjaya). Around 100 different sakes at any given time, plus
good food. 03-3410-9918. Sangenjaya 2-15-3.
Sasagin (Yoyogi-Uehara). An impressive selection of sake and traditional
izakaya-style food. 03-5454-3715. Uehara 1-32-15.
Awamori
Nabi to Kamado (Shinjuku). 300 awamori varieties and decent food. 03-5379-1070. My City 7F.
Awamori (Ginza). 150 different types of awamori. 03-3543-9256. Ginza 7-17-18.
Aka (Akasaka). Okinawan fusion cooking and 22 awamoris at this late-night
bar/restaurant. 03-5157-0909. Nagatacho 2-14-3, Akasaka Tokyu Plaza.
Shochu
Tamoiyanse (Shibuya). 50 kinds of shochu from Miyazaki/Kagoshima, including
types made from sweet potatoes, barley, corn, rice and sugar cane, plus excellent
southern Kyushu cooking. 03-3461-4333. Shinsen 10-10.
En-ichi (Nishi-Azabu). Over 700 kinds of shochu (how is that even possible?) and Kyushu snacks to go with them. 03-3499-0233. Nishi-Azabu 4-10-3.
Australian wines
Mr. Zoogunzoo (Omotesando). Excellent French/Italian cooking and a very
extensive, very reasonably priced wine list. 03-3400-1496. Shibuya 2-9-11, Aoyama
City Bldg. B1F.
Arossa (Shibuya). They boast a solid regular list and an impressive reserve
list for special occasions. Several are available by the glass at any given time,
with good Italian/Australian food. 03-3469-0125. Shoto 1-26-22.
California wines

Ricos Kitchen (Ebisu). Not the biggest list in town, but the 40 California
wines here are well chosen, and the food is superb. 03-5791-4649. Ebisu 4-23-7,
2F.
New York Bar (Nishi-Shinjuku). The biggest California wine cellar in
Asia, with snacks from the kitchen of the adjacent New York Grill; prices match
the 52nd-floor view. 03-5323-3458. Nishi-Shinjuku 3-7-1-2, Park Hyatt Tokyo 52F.
French wines
Aux Amis des Vins (Ginza). The wine list here is the size of a small phone
book, and they're open late. 03-3567-4120. Ginza 2-5-6.
Bandol (Gaienmae). 70 wines, mostly imported by the owner, plus southern
French cooking. 03-5785-3722. Minami-Aoyama 2-12-16, Ishizuka Shoji Building 2F.
AOC Yoyogi. Organic French food and dozens of organic wines. 03-5308-7588.
Yoyogi 1-43-2.
Italian wines

Caminetto (Gaienmae). Over 100 types from Tuscany and Piedmont (priced
Y3000-20,000), and excellent food. 03-3479-7553. Kita-Aoyama 2-7-18.
Other wines
Sherry Club (Ginza). An astonishing variety of sherries, with Spanish
tapas to go with them. 03-3572-2527. Ginza 6-3-17, Yugen Bldg. 2/3F.

Manuel (Shibuya). A Portuguese restaurant with a reasonable selection of
after-dinner Port, plus several Portuguese wines. 03-5738-0125. Shoto 1-25-6.

Cave de Katsunuma (Shinjuku). Western-style food and a large selection
of Japanese wines, for the curious. 03-3225-4101. Shinjuku 3-11-10, B1F.
Belgian beers
Brussels (Nishi-Azabu). The most spacious branch of the Brussels mini-chain,
with the best food menu as well. 03-5413-5333. Nishi-Azabu 3-21-14
Frigo (Nishi-Shinjuku). 100 Belgian and German beers, all available for
inspection in the self-serve refrigerator. 03-5371-0666. Yoyogi 2-11-20, B1F
Bois Cereste (Akasaka). An old-school Tokyo bar with live piano music
and around 100 Belgian beers, many exclusive imports, plus Belgian food. 03-3588-6292.
Akasaka 2-13-21.
German beers
Bernd's Bar (Roppongi). Several German beers on tap, good food and a lively
atmosphere. 03-5563-9232. Roppongi 5-18-1, 2F.
German Farm Grill (Shibuya). A casual bar/eatery with a few unusual German
beer brands. 03-5457-2871. Shinsen 8-1.
Japanese microbrews
Popeye (Ryogoku). The largest selection of Japanese microbrews in the
world. The 40 beers on tap also include US and European craft beers. 03-3633-2120.
Ryogoku 2-18-7.
Glossary
Shochu - distilled spirits usually made from sweet potatoes, traditionally
popular in Kyushu.
Awamori - distilled liquor from Okinawa.
Aquavit - flavored liquor distilled from grain and served ice-cold, popular
in Scandinavia.
Grappa - brandy distilled from grapes, popular in Italy.