I think its a problem probably because of this CleanMyMac 3 app that says i have got only 100mb from my 8gb and when I click on "Free Up" I get more than 3gb free RAM only to fill it again after a while. The only thing feels slow on my system is when I enable the Transparency effects the minimizing and dragging the apps windows seems utterly slow (lagging).
I tried to install fresh copy of Yosemite and it was smoother and the lag was gone but I have to use this system so restored it. That's why I think some apps are causing this issue?

As you can see only 100MB of RAM is free!

My Mac specs:

EtreCheck report as advised: http://pastebin.com/rxuGqef6