Onsens

In Kumamoto city:

Batten no Yu (ばってんの湯)
http://www.battennoyu.com/
Google coordinates: 32.775517,130.738206

Suishun 〔水春温泉〕
Yes yes and yes. This place is awesome. Great water, great atmosphere, and the ganbanyoku is amazing.
http://suisyun.jp/kashima
Google coordinates: 32.736606,130.748806

Tsuru no Yu (つるノ湯)
This onsen is right next to KK Wing, so if you spend a couple hours jogging there, you can hit up the onsen afterwards. Awesome!
http://www.turunoyu-t8.com/
Google coordinates: 32.842268,130.7811

Ikkyu  (一休温泉)
http://www.19-onsen.com/
Google coordinates: 32.790319,130.776181

Yu Rakkusu (湯らっくす)
http://www.genkysquare.com/onsen2/onsen.html
Google coordinates: 32.785304,130.702415

Shiro no yu (城の湯)
http://www.shironoyu.co.jp/
Google coordinates: 32.810975,130.701642
This onsen is very close to the castle.

Onsens outside of the city:

Kafutei Onsen(花富亭 温泉)
http://www.kafutei.co.jp/
Google coordinates: 33.024209,130.780946

Green Pia Onsen〔グリーンピア温泉〕
Best view from an onsen. It REALLY is breathtaking.
http://hgp-minamiaso.com/index.html
http://hgp-minamiaso.com/fasilites/onsen.html
Google coordinates: 32.801416,131.036976

Akagawa 〔赤川 温泉〕
http://www.akagawaonsen.com/index.php
Google coordinates: 33.053637,131.229237

Kikunan Spa Resort: Anganasse (菊南スパリソートあんがなっせ温泉)
Most classy, make-you-feel-rich onsen in all of Kumamoto. Go there once to feel like a king. It does cost 1400 yen though.
http://agannasse-spa.jp/
Google coordinates: 32.860425,130.727809

Tarutama Onsen (垂玉温泉)
An amazing onsen with a traditional feel.
Google coordinates: 32.862565,131.035672

Jikoku Onsen (地獄温泉) 
This is a famous onsen. Famous for its mud. The main muddy baths are mixed, and ladies its ok to wear a towel in the water.
http://jigoku-onsen.co.jp/
Google coordinates: 32.860204,131.036155

Hot sand bath  
http://www.ryuusenkaku.com/index.html
http://www.jalan.net/yad367018/
Google coordinates: 32.956285,130.727175

Onsen Towns 

Kurokawa 〔黒川温泉〕
Possibly the nicest and most famous onsen town in Japan. People come from near and far to enjoy the wonderful atmosphere and onsens there.
http://www.kurokawaonsen.or.jp/english/
Google coordinates: 33.078139,131.142039

Yufuin 〔湯布院〕
This town has wonderful Autumn leaf viewing. Good to go here in the fall for onsen and autumn leaf viewing.
http://yufuin.or.jp/global/index.php?easiestml_lang=en
Google coordinates: 33.26607,131.368246

Beppu〔別府〕
http://english.beppu-navi.jp/
Google coordinates: 33.280028,131.507807

Ibusuki (指宿)
This is a hot sand bath town. The sand along the beach is heated by volcanic activity below. You can get buried in the warm sand on the beach, cook, and enjoy the view of the beautiful mountain ranges across the sea.
http://ibusuki.or.jp/
Google coordinates: 31.223078,130.655422

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