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 it's 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 suck 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?