Can I make visa runs from Japan?

I'm 24, from EU, currently on a tourist visa in Japan. I got my ARC, I work as a freelance web designer from home, I get paid by oversee companies and I would like to stay in Japan longer.

Is it possible to do visa runs from Japan? I mean, at the end of my 90-days stay go abroad for a couple of days, return and get another 90-days tourist visa?

The first time you do this it is likely, although not guaranteed, that you will be allowed in again. If you try to enter Japan a third time within a one-year period after having stayed 90 days on both previous entries, chances are very high that you will be turned away at Immigration and not allowed in for another 6 months.

There is an unwritten limit of 180 days in any one year. Sometimes there are exceptions to this, but they seem to be getting less and less common.