Top 3 affordable places to live in Japan

I am applying for the JET program and I want to know the top 3 places to live in Japan. I dont want to live in any large city with expensive rent. Do you have any suggestions?

You can't really expect a useful answer based on that post.

First, you're applying for JET, which as far as I know means there are no guarantees about placement.
Second (and this is true of ANY country), outside of major cities, most cities are inexpensive.
Third, you provide absolutely no useful information.

Your college professors would through a book at you if they knew you communicated this way.

How about thinking up an organized, though-out question and give it another go?
Otherwise you're wasting time.

Basically anywhere that is a long way from a large city will be relatively cheap- I doubt it's possible to pick an actual "least expensive 3" out of all the thousands of small towns/villages in Japan.

Even within the same area, rents will vary quite a lot depending on the size of the apartment, age of the building, distance from a station etc.

You might want to consider instead what kind of climate you would like to live in- I know a person who was placed by JEton Rishiri island off the northwest coast of Hokkaido where the winters are long and freezing and summers are cool, and others who were placed on a small Okinawa island- both probably have similar rent costs but would be very different experiences.

You might want to factor in how much it might cost you if you ever do want to get to a larger city to do some shopping/meet up with other English speakers etc- long distance transport can be quite expensive here, and possibly cancel out what you save on rent if you go very often.

Your college professors would through a book
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I think the same college professors might "throw" a book at both of you. :=)

Even in large cities rent isn't the same across the whole city for apartment of the same type /size

The rent for a apartment of X square metres vary hugely from one area in a city to another, and even between streets within an area, not to mention the age of the building, amenities (or lack of) in the building, distance from shops, transit etc.

Where I live a 1 bedroom apartment of 60 sq metres can rent from $ 600 to 2000 plus!!

No wonder books were always flying in my direction ;-p