Sticking to your question, I believe that Mendeley and Zotero are the most commonly used because of their free features (with the latter being entirely free). However, the prevalence of their use does not tell you at all about the comparative performance of these softwares in fulfilling completely the reference management needs for systematic reviews with or without meta-analysis. If you limit the population of interest to full-time or veteran researchers, I won't be surprised to see EndNote at the top of the list.

Mendeley

Mendeley

Also worth checking Paperpile with gdocs plugin.

EndNote

Mendeley