The great thing about the Japanese breweries is that they all produce local specialties. This beer is only sold in that particular district and the best way to taste it is to visit the local brewery itself. I have been to a couple whilst I was living there and they give about 45min to chug down as much of their brew as you can. Tours are free, so if you're heading to Japan, pick up a railpass (buy before you go) and then hit the breweries. There are lots of breweries around. Only some have English speaking guides, but you don't need to speak Japanese to enjoy the beer!
I wasn't a big fan of Yebisu, as I prefer black beers. Both Kirin and Asahi produce black beers (kuro-nama) but they aren't widely available. Another anomaly of the Japanese brew scene is Happoshu which is a beer flavoured alcoholic drink. Because beer is taxed on the amount of malt it contains, the Japanese have found a way of brewing a beer as a flavouring then adding this to a tasteless carbonated liquid to produce a cheap alternative to real beer. It gives a shocking hangover, but costs about half the price of real beer. Given the cost of beer in Japan, happoshu is very popular.
Joe