Transportation for Longer-Term Visitors

I know that Japan already has many fantastic transportation packages for non-Japanese visitors on a temporary travel visa, but what options exists for longer term stay?

I will be studying abroad in Japan for a year next year. I'll be close to Osaka and I would like to be able to travel around a little bit (Hiroshima, Nagano, Tokyo, maybe Sendai) without breaking the bank, especially considering the prices of the bullet train or distant travel in general in Japan.

I have been to Japan before on a temporary visa and have used, and am familiar with, passes like the JR Rail Pass, the Kansai Thru Pass, and IC cards.

Are there any similar options available to long-term visitors/students or what do Japanese do when they travel? Because I'm a university exchange student I'm barred from driving a motor vehicle, so any information on public transportation or affordable flights would be greatly appreciated.

Thank you!

Yes, there are many discount train tickets which are available to everybody. Some are advertised in English such as the Seishun 18 or the Tokunai, but there are many more. Consult the companies' websites and look for お得 (or おトク), meaning "discount". For example

http://www.jreast.co.jp/tickets/
http://railway.jr-central.co.jp/tickets/index.html
http://www.jr-odekake.net/railroad/ticket/tokutoku/

The Tokyo Wide Pass and the N'EX Tokyo Round Trip Ticket are also available to all foreigners, not just to tourists, and JR Kyushu has a pass for foreign students.

https://www.jrkyushu.co.jp/tabi/2011_study_abroad_pass/index.jsp

Of course, highway buses and low-cost flights are also available, they are well-documented here and elsewhere.

Thank you, this is exactly what I was looking for!