Question about visa

Is there a limit for the number of time a tourist visa can be renewed?

I went to Japan last September on a 3-month "temporary visitor" visa, then after these 3 months, I went to the Immigration Bureau (don't know the exact name for that in english), and extended the visa for 3 other months. (So for a total of 6 months).
So they stamped the extension permit until February into my passport, but also a red
"�¡‰ñŒÀ‚è�@Final Extension" Stamp.

Does that just means that I couldn't extend it further that time, but it was okay if I left Japan then comeback?
I will go back to Japan this summer, and I suddenly remembered about this stamp, so I became a little bit worried... What if the deny me entry this time?

That's right. Swiss people can extend once to a total of 6 months. After that they have to leave (or change their status of residence to a different one, e.g. student, work or spouse).

Since you will have spent several months outside Japan by that time you should be fine coming back in. If you had left and then tried to come back within a month they might have been suspicious, but in your case you shouldn't have a problem.

So, I was able to come back to Japan today,
but the stopped me at the immigration, and told me that since I extended my visa last time, to six months, and am now coming again for two months, my time in japan exceeds 6 months in the span of a year and thus could not be considered "Temporary".
They let me in anyway, because I could prove that I will really leave at the end of August, and had relatives that could take guarantee for me.
But they also told me that if I was ever to come back to Japan, I will have to be very careful about what visas to take and such, and I will have to wait at least 1 full year before applying again.

I was actually considering going to a Japanese University starting 2012, but I wanted to come to Japan in 2011, and work a little bit while improved my Japanese.

For this, I wanted to apply for a "Working-Holiday" visa, that I could obtain from France, as I have French and Swiss double-nationalities.

Can the fact that I was warned this year influence negatively the procedure of getting a visa later?
And also, as I already came to Japan twice with my Swiss-nationality passport and registered as such, will it be possible for me to come again with a visa obtained through anyother country?
Or will it be considered as a tentative of fraud?

No, it should have no influence. After all, they even told you to go for a proper long-term visa the next time.

As for using the Swiss passport, as long as you have the proper visa, shouldn't matter.

But what if you used French passport? Well, they do that fingerprinting thing now, so what if it counted as fraud or something, trying to use different passports back to back?

If you waited more than 6 months, then using the french one the next time should be fine.

If you come back on a Working Holiday Visa, that should be fine. Just be careful, though, I think there is a requirement to have lived in the country of your passport (so in your case France) for a certain period of time before you can apply for Working Holiday Visa.