What is the longest-running manga series that has already ended before september 2016?
The series mentioned by senshin in the comments are hard to beat. But here is a new record:

Chiisana Koi no Monogatari (小さな恋のものがたり) ran for 52 years, from 1962 to 2014.



It was created by Chikako Mitsuhashi and published by Manga Time. A total of 43 were published.

Sources: wikipedia and myanimelist.

According to the same wikipedia article, the record to most chapters seem to go to Sazae-san, with 6477, and the one for more volumes published to Nijitte Monogatari with 111.