There are so many beer and Oktober fests in Japan, I cannot possibly list them all here. But I do have some suggestions. Prosit!
Akihabara Oktoberfest
Where: Akihabara
When (expected): late March – early April
Website: www.inter-fc.org (in Japanese) 
Image courtesy of amiamiblog.com
Nagoya Oktoberfest
Where: Hisaya Odori Koen, Hisaya Hiroba, Nagoya
When (expected): May
Website: http://nagoya-oktober-fest.com (in Japanese)
Hibiya Oktoberfest
Where: Hibiya Park, Tokyo
When (expected): September
Website: http://www.oktober-fest.jp/hibiya/ (in Japanese) 
Image courtesy of japan-attractions.jp