Kikuchi Gorge (菊池渓谷)
Mentioned before. Nice hiking. Beautiful, fresh, and cool (its always a little chilly there, year-round)
Google coordinates: 32.784571,130.734274

Aso-san (阿蘇山)
The famous volcano in Kumamoto. Its worth a visit. There is some good hiking to be done there. It’s fun hiking there in the winter in the snow.
Google coordinates: 32.886507,131.082662

Shirakawa Suigen 〔白川水源)
This is an amazing freshwater spring. Tasty water!
Google coordinates: 32.825654,131.095219

Takamori Yuusui Tunnel  (高森湧水トンネル)
They were digging a train tunnel and hit a spring, and they gave up on the project. Now you can go into the tunnel, enjoy the cool air, drink from the spring, and enjoy a neat water show.
Google coordinates: 32.813806,131.122534

Nabegataki (鍋ヶ滝) NO BUS??
This is a beautiful waterfall that you can walk behind. During certain times it’s lit up at night. Check out the amazing pics online.
Google coordinates: 33.136886,131.035566

Kujuu-san (九重山)
There is lots of hiking to be done in the Kuju area. There is a onsen that is in the middle of the mountain range and it can only be accessed by hiking trails. Pretty cool!
Google coordinates: 33.097941,131.255121

Kujuu Yume Outsuribashi (九重夢大吊り橋)
This is the longest foot suspension bridge in Japan. Beautiful views.
Google coordinates: 33.173848,131.226754

Takachiho (高千穂)
This is an amazing gorge. You can rent rowboats and paddle around in it.
Nearby there is also a cave that has many stone statues in it. I believe that the Gods that created Japan are from this area. Pretty cool. There is also a temple in the area that is nice. During the summer they light up the gorge at night with colored lights.
Google coordinates: 32.701655,131.302328

Underwater caves[稲積水中鍾乳洞 (いなづみすいちゅうしょうにゅうど)] NO BUS?
There are underwater caves. Pretty cool! There is also a nearby Showa Era town.

Unzen and Fugen dake Mountain / Volcano (雲仙)
Unzen is a hotspring town that has a very European (German and Dutch) feel. There is nice hiking to be done around the Fugen Dake volcano.
Google coordinates: 32.813806,131.122534

Harajiri no taki (原尻の滝)
This waterfall is called the Niagara Falls of Japan.
Google coordinates: 32.964189,131.450794

Kirishima (霧島)
This is a beautiful volcano rich region in Kagoshima. Nice views and great hiking. It’s a very famous place. It’s also famous for its onsens.
Google coordinates: 31.929438,130.844421

Sogi no taki (曽木の滝)
Really beautiful waterfall in Kagoshima.
Google coordinates: 32.01237,130.576372

Yakushima (屋久島)
A beautiful island south of Kagoshima, famous for its hiking and beautiful trees.

Crazy big tree (寂心さんの大クス)
Google coordinates: 32.871676,130.684412

3333 steps! 
If you have ever wanted a physically demanding challenge, or have wondered what fiery jello legs would feel like, this is the hike for you. There is an amazing view from the top and a very old temple.
Google coordinates: 32.577123,130.82305

Check out this webpage for some awesome bridges.

Hiking, hiking, and more hiking info. Ask a teacher to help you if you are interested in a place. Also, check out Lonely Planet’s hiking Japan book.