File management - how do you handle your library files?

So, I've crossed the 1000 movie threshold.  With that, I've had to expand my data storage.  My question for everyone is "how do you store your library files?"

What I mean is, do you put all 1000 movie folders into a single folder called movies?  Or do you somehow break it up for file management purposes?  For purposes of this question, I'm not talking about anything within the Plex Media Server, I'm talking about the straight file structure on your server.

I'm just looking for best practices.

Thanks,

Mike