Thank you Frank, I have thousands of files created everytime, so I will try to see if excluding the JS is worth it.
As for the cache managed by other services, I don't understand, how they are suppose to delete the created files by themselves?
I'm using W3 Total Cache next to it, but currently considering WP Super Cache instead. How do I "connect" them to have the files created by Autoptimize (stored in wp-content/cache/autoptimize) managed by my caching plugin?
thanks
Razique