Strong Japanese small town/village setting

[Kameruka]

Upon watching Yosuga no Sora, I was impressed to see how beautiful the Japanese village looks like. In fact it was partially based on a real village. I don't really care what genre they are but I think harem and slice of life genre are given highest priority. Please no yaoi and shounen-ai regardless how well-executed the Japanese small town/village setting they are.

[Simon]

These aren't exactly what you had in mind, but they might be of interest:

• Kamichu! Set in a small city on the cost of the Inland Sea, but very much about Japanese tradition and the place of Shinto gods in the modern world. Or you can just enjoy it as a charming slice-of-life with cute, likable characters.
• Windy Tales Again, mostly in an urban setting but there's key back-story around the village one character comes from and the traditions / obligations he brings with him (most of one episode is set there, in fact). The abstract character designs put some people off, but if that doesn't bother you it's a great little story: in true Nishimura Junji style there's a lot going on behind the apparently simple plot. Also, if you're interested in the strong family ties of village life, this anime is noteworthy for not just showing the main character's parents but actually having a whole episode about them.

[GreatTeacherKen]

Air TV- supernatural drama series set in a small town. Unfortunately, the real life place the setting is based on doesn't exist anymore, but it looks absolutely gorgeous in the series.

My Neighbor Totoro- slice of life movie set on a farm. As can be expected from Studio Ghibli, the scenery is lovely.

Only Yesterday- another slice of life movie from Studio Ghibli, the present day scenes in the story take place on a farm.

Onegai Teacher and its sequel Onegai Twins- romance series set in the countryside. Scenery is quite lovely as well, especially in the opening animation.

[SeijiSensei]

I'll recommend Ghost Hound, an excellent show set in a small rural town.

[MeoTwister5]

Series wise, I will definitely second Air TV, Kamichu!! and Windy Tales. You should also try out Tamayura.

[thevil1]

Please Twins

Higurashi No Naku Koro Ni

[margafred]

Lets see....

- Natsume Yuujinchou <-- Absolutely recommended.
- True Tears <-- Another great series.
- Sketchbook ~full colors~ <-- Somehow might fit into your description
- Asatte no Houkou
- Tamayura <-- New series. Absolutely recommended.
- H2O: Footprints in the Sand <-- Beware of trap.

Hmm... can't remember of anything else for now. Guess this 6 will do for you for now.

[seintsu]

Nagasarete Airantou is a harem anime set on a remote island. The setting is supposedly a small Japanese village that was cut off from real society about 120 years ago.

[qwertyuiopz]

ghost hound

[Guardian Enzo]

Thirding Ghost Hound.

For me, Zettai Shounen has the most memorable small town setting of any series - Tama is really almost like a character in itself. The second arc is in Yokohama, however. Very slice-of-life as well.

Natsume Yuujinchou has a nice small-town setting. Gentle, wistful and quite a beautiful show.

Shiki also have a distinctive small-town setting, though it's a 180 degree shift from the shows above. Dark, scary and morally ambiguous.

[totoum]

Seconding 3 shows:

True Tears
Sketchbook Full Color's
Shiki

That makes 3 different genres , Drama/Romance,Comedy/Slice of life and Horror.

[Haak]

I will second Shiki, Air, My Neighbour Totoro and Only Yesterday.

I also think Summer Wars counts and Durarara!! is good for a strong city setting if you're interested.

[Falkor]

seconding Tamayura and Sketchbook. I would like to recommend ARIA (Animation, Natural, Arietta, Origination), even though the settings is not in a Japanese small town/village. the atmosphere, the mood, how the city of Neo-Venezia becomes part of the story, I think you will enjoy these elements of the show.

[SuzushinaYuriko]

Higurashi no Naku Koro ni and Shiki if you want dark anime. Specifically, Higurashi relies more on the shock factor from the get-go while Shiki starts off slow and slowly builds up the creepiness. Higurashi is more of a murder mystery anime and Shiki is more of a horror anime.

Seconding AIR. Also, Durarara!! doesn't take place in a small village but in modern day Ikebukuro, but the backgrounds for it are EXTREMELY close to their real life counterparts. Someone actually went to Ikebukuro and took comparison photos which can be viewed here, but beware of slight spoilers if you decide to click it.