Before the Animesuki board was reset, there was a couple of threads on this.
The sites appear to be in Nagano Prefecture, Honshu.
Most sites (at least around Maiku's house) are at Lake Kizaki and Omachi City.
And while I'm not 100% sure, I think the school is in Matsumoto.
Here's a site with photo comparisons of real vs anime:
http://www5d.biglobe.ne.jp/~kazeyama...o/one2sato.htm
Ane here's maps and more pictures of the area:
http://j-music.fuzzy2.com/onetei/00kizakiko_bgm.html
It probably doesn't look typical because it's a resort area.