God, I'm glad I found you guys.
I was suffering this problem for more than a month now. Whenever I checked the Console after every reboot, there were no explicit issues.
I had a feeling that I started to suffer these freezes after 10.11.4, then I waited for a quick update since I thought that a lot of people would be impacted. The update never came, which made me believe that I could be the only one.
So I took my macbook for repair, but the guys couldn't reproduce the freezes. I got my macbook back and boom, frozen once again.
I decided to format my macbook as a last resource last night. Now I'm clearly suffering the issue when trying to watch videos, along with the clear message in the console mentioning that the video decoder is stuck.
The point is that now the freezing circumstances are clear after formatting my macbook - this enabled me to find this thread. Probably the fact that I had VLC player before formatting was masking the diagnose somehow.
Nevertheless, I'm really upset with all this. I thought my macbook was defective and I was annoyed that I could not diagnose anything, neither the repair guys.