There are a million degrees of underground.
Womb (Shibuya), Ageha (Shinkiba, free shuttle bus from Shibuya).
Big underground clubs.
I like Unit (Daikanyama/Ebisu) and Eleven (Nishi-Azabu) much better than Womb, personally.
Air (Daikanyama) and Warehouse (Azabu Juban) are also pretty good.
Liquid Room in Ebisu is also good.
Nuts and Harlem (both Shibuya) are alright, mostly Hip Hop.
Club Asia (Shibuya) check the schedule, wide variety of events
Smaller but good vibes.
Trump Room (Shibuya) skews Electro
Game (Shibuya) skews house and dubstep
Family (Shibuya) skews hip hop and dubstep
Module (Shibuya) skews house and techno
Fai (Aoyama) skews house, techno, electro
Room (Shibuya) skews jazzy, and house
Loop (Aoyama) skews house and techno
Ever (Aoyama) is electro, but I'm not a fan of the vibe here.
Hachi (Shibuya) skews house and techno.
Free entry and small
If you're looking for a free entry, but cool place to hang, try Bonobo in Harajuku (Sendagaya), or Oath, just outside of Shibuya about 1km towards Roppongi. Theres usually someone good DJing on Friday and Saturday at these places and vibes are always good.
Super-Deluxe (Nishi-Azabu) although they aren't a club as much as a multi-purpose performance space. Many live events, some club events, some performance events, etc.
I use the word "skew" above loosely as most clubs have a wide variety of events. Best!
Really appreciate this list man. I'll be moving to Shinjuku next month (been living in Hokkaido for the past two years), so I can actually get cabs home without spending TOO much money (since so much is happening in Shibuya). I've always preferred a smaller/more intimate club setting than a superclub -- although WOMB always has DJs I like. Definitely gonna run through your list as soon as I get down there. Cheers.
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Adding to the list:
"Sound Museum Vision" is a large, newish club in Shibuya run by the Air people.
Also Eleven (Nishi Azabu/Roppongi) is more or less "Yellow" re-opened with a somewhat weaker sound system. Still they have some big names go through there.
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thanks for the list, excited to visit Oath and Womb!