I want to refactor the files and directories on my system. However I am not sure what is best practice.

After reading this question and its answers I assume the most important part is to be consistent. However, this is where I'm stuck. E.g. in root, there are directories such as /bin and /usr, which all use lower-case letters. But in my user's directory /home/foobar/, there are already a bunch of directories such as ~/Pictures, ~/Documents and ~/Music (which are capitalized)!

Maybe this is just because I use Ubuntu, but what is considered best practice?