Here are a list of some good arcades to check out:
Club Sega Akihabara
http://location.sega.jp/loc_web/images/tokyo/cs_akihabara01.jpg
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Directions: Go to JR Akihabara station, exit “Electric Town Exit.” Walk out of the station and hang a right – you should see the “Die Building” – and keep walking straight. Club Sega is across the street.
Info: They have five floors of games, with the basement being all Virtua Fighter 5 and the 4th floor primarily GGXX AC and Street Fighter. The 3rd floor is mainly Tekken 5: DR, but they also have a SC3 machine as well. 5th Floor is dedicated to Gundam games. The SF community has a strong presence here, but it’s mainly a VF area.
Club Sega Shinjuku Nishi
http://location.sega.jp/loc_web/images/tokyo/cs_shinjukunishiguchi01.jpg
Directions: From JR Shinjuku or Odakyu Shinjuku, head to the West exit (Nishi Guchi). Walk towards the Bus Terminal going to Shizuoka and other prefectures and you’ll see a Yodobashi Camera right behind the terminal. Behind Yodobashi Camera is Nishispo.
Info: Basement is split up between T5DR, VF5, Gundam, GGXX AC and Gundam. Basically, the basement is the ‘battle arena’. The top floors are for other games that aren’t as popular or are single player, and they also house the card battle games (Sangokushi Taisen, Quest of D, etc.) The level of competition is very high here as well. It’s probably the best if you want to play VF5 and Gundam.
Ikebukero Gigo
http://location.sega.jp/loc_web/images/tokyo/ikebukuro_gigo1.jpg
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Directions: From JR Ikebukero station take the East exit and head straight for about 5 minutes, and you’ll find Gigo.
Info: They only list VF5 as their main game in this arcade, but the arcade is known for its strong Guilty Gear community, and I heard that the other 2D fighters (Arcana Hearts, Melty Blood, 3s, etc.) are very popular here as well. Most of the fighters are located in the basement, last time I was there. I should also mention that if you pick up any issue of Arcadia magazine, they give a listing of arcades in specific areas. They choose a different city each issue, but it’s usually within the Tokyo area since it’s the most populated. Check it out if your Japanese ability is high enough.
Hope that helps.