Searayman,
Don't take this as a flame, but once you're rooted you've become a real danger to your phone. I'm not sure you understand exactly what you've done, but you have in essence become the system administrator for a very complex multitasking operating system. This allows you to literally destroy that operating system by removing files and folders.
Yes, you can "clean up" some of your media folders. But you could do that without being "rooted." Now there are literally no constraints on what you're able to do to your file system. Unless you fully understand the way the android o/s works, DON'T MESS WITH YOUR FILE SYSTEM beyond what you can do as an "unrooted" user.
This is why for many years the "root" password on Unix systems (the ancestor of your phone's o/s) is jealously guarded by a system administrator and not handed out to every user of the system. With "root" privileges, a user can literally order the operating system to delete itself.
If you have an extra phone, a complete backup of your files and folders (and a way to recover them), and the time and energy to learn what you can safely delete, go for it. But if you've rooted your phone by using one of the handy dandy utilities floating around out there and don't know much more about your file system than what you can guess from the file structures and programs the "rooting" placed on your phone, get therapy for your OCD.
Rant off.