Visa applications

I have been in Japan for few months as a trainee, I found a girlfriend there and now have a pregnancy. I'm at my home country now and I want to go back Japan to marry my girlfriend, live with her, work there and rise our future kid.
Which kind of visa should I apply?
Any important procedures needed?
By having a kid in Japan (newborn but not yet married my girlfriend) have a positive concern in visa applications?

Enter as a tourist.
Get married.
Apply for spouse visa.

The problem will be how to obtain a tourist visa, as OP probably needs one.

Since you are not yet married, you will probably be applying for a Temporary Visitor visa. (Without knowing your nationality, we don't know if you are eligible for a Temporary Visitor Visa waiver or not.)

Once you are in Japan, (1) you get married in Japan, then (2) apply for resident status change to Spouse of Japanese National.

So before you leave your home country, be sure to check what documents you need to:
(1) get married in Japan according to the Japanese law. Your girlfriend in Japan can inquire with her city hall exactly what you need. Often you are required to have certificate of no impediment to marry (paper stating that you are not married now), birth certificate, etc.
(2) apply for change of resident status to Spouse of Japanese National. Again ask her to check the Ministry of Justice's website to see what you/she need. The summary in English is here (scroll all the way down to see "Spouse and Child of Japanese National"):
http://www.immi-moj.go.jp/english/tetuduki/kanri/shyorui/Table3-1.html