Thought I should finally get around to posting about my amazing Japan trip. I didn't get to as many beer places as I had planned but in Tokyo I made it to the following:
Popeye's -
http://www.lares.dti...lish/index.html
http://beeradvocate....1/?view=beerfly
Probably the best beer bar I went to in Japan and it's a must visit. Was a comfortable, dark, slightly-divey pub with 70 taps of American beer, Japanese brews and also some Belgians. I was there from around 6 on a Tuesday night, it was half full and quickly filled up with a great friendly atmosphere and cheap and tasty Japanese-style bar snacks to boot.
The Bairds taproom at Nakameguro -
http://bairdbeer.com...ameguro-taproom
http://beeradvocate....r/profile/17971
This pub was a lot of pine & chrome so felt more like a pizza hut than a pub but the Bairds beers are really good, they had 3 handpumps in operation and served good pizza. I stopped in around 2pm with 3 non-beer drinkers who weren't keen for a session so I wasn't able to stay for long and that may have detracted a bit from my enjoyment. Worth a look if you're in the area and Bairds have a few other taprooms around Tokyo.
Ant n Bee in Roppongi -
http://www.ratebeer....nt-n-bee/22129/
http://ameblo.jp/rop...beerbar-antnbee
This bar is a windowless underground bunker but the taplist was good with Japanese IPA's and other brews - I even tried the cherry blossom "sakura IPA" which was interesting. Right next door was a bar called "Hollow Point" where you could shoot air rifle AK-47's, M-60's and 357 Magnums so that was pretty good fun. Roppongi is apparently the red light district but, other than being accosted on a corner for a few minutes by a Nigerian spruiker who wanted to take me to his club, it seemed pretty tame.
There's a great bottle shop I went to called Tanakaya -
http://beeradvocate....er/profile/3433
Big selection of US, Japanese, German, Belgian etc and cheap. Was the best bottlo I went to and also had a huge wine & scotch selection if that's your thing.
In Tokyo I was staying in Ebisu and there was a supermarket upstairs from the Ebisu train station which had Bittburger 500ml cans, duvel, orval and two great beers from the Japanese Yo-Ho brewing company, Yona Yona ale - an American pale ale for $2.39 a can and Aooni - a 7% American IPA for $2.89 or so (it was about 100 yen to the dollar while I was there so it was easy to work out how much I was spending). Beer & food is super-cheap as compared to here.
I stocked up on heaps of these as takeaways and they were delicious. I had plans to get to Craftheads and The Watering Hole but unfortunately didn't make it.
Besides Tokyo I went to Hiroshima, Osaka, Kyoto, Nara, Fujiyama, Takayama and Kanazawa. I didn't get to go to any beer places in these areas and had to make do with supermarket beers. Of these I found Yebisu Premium and Suntory Premium Malts to be the two picks of the bunch. Had a few beers at a baseball game at the Tokyo dome from this nice lady:

The beer vending machines I'd heard so much about weren't as plentiful on the street as I had been told - apparently there's been a crackdown on underage drinking - but you'll see them here & there and vending machine beers were only $1.10 to $1.80 for a 500ml can.
I did heaps of sightseeing and was lucky enough to land right in the middle of cherry blossom time which was incredible.

Sharing a beer with a deer in Miyajima:
The Kirin headquarters in Tokyo. It was designed to resemble a golden beer with frothy head which is pretty awesome. No one seems to know what the sculpture next to it is supposed to be so everyone just calls it the golden poo:
Throwdown-style cans at the local discount store for 77 cents:
It was a fantastic experience, the people were super friendly and I had an absolute a ball.