While Mos Burger (see thread below) is good comfort food (great for hangovers, and they are EVERYWHERE), for a great burger in Tokyo - the kind of burger that you actually plan your evening around - try the following places (ranked in order of quality):
1. Ha'apuna - Omotesando
These burgers are everything that one would expect a burger to be...thick, juicy, and cooked to order. The flavor of the slightly seasoned meat (brought in fom the USA) is definitely worth the cab/subway ride. They also offer about 15 different toppings (cheddar cheese, avocado, grilled onions, sauteed mushrooms, jalapenos, hickory smoked bacon, etc...) which allows you to create the burger of your dreams (At least, by Tokyo standards). And the toasted poppy seed buns are wonderful. There is no weird "special sauce" glopped on the burger. Each table has a bottle of ketchup, French's mustard, a jar of really nice dill pickle chips, and (at request), mayo.
2. T.Y. Harbor Brewing Company - Tennozu Isle
(Full disclosure - The chef/manager at this place, David Chiddo, is a buddy of mine). At 180 grams, this is probably the biggest single patty in Tokyo. The meat, which is automatically topped with cheese (but you can ask for it without) is really, really flavorful, and quite juicy. Each burger is served with - on the side - tomato, red onion, and 1/6th of a head of lettuce...go figure. The spiced mayo sauce (in a dish on the side), is quite nice, but their bacon is a bit lackluster. Each burger also comes with a HUGE order of french fries. David wasn't really happy with the buns he was using, so, one morning, he staked out Ha'apuna during their bakery delivery, and now both places use the same buns. Big Plus - T.Y. Harbor's main business is as a microbrewery (of which David has no part). Check out their amber ale!!!
3. T's Diner - Meguro
This 50's style diner just opened about a month ago. If you sit at the counter, you can watch the chef hand-form you burger. The fat content in these burgers is obscene, but makes for a great meal. The buns are good old-fashioned sesame seed, lightly coated with a "Secret Sauce" (read: 1000 Island). The thing that makes T's worth going to is the chili (extra) that you can have put on it. This stuff has a kick that will have you ordering another chocolate malt faster than you can say "Excuse me, can I have another chocolate malt?" Also, the jukebox is FREE.