I've had the same thoughts many times. It is a never-ending work in progress.

Problem #1: I like too much, but I will never have enough time to watch/read/play/listen to it all in my lifetime. I need to be more selective with the content and keep only what I love and start deleting the average/OK stuff.

Problem #2: Most of the re-encoding done is because of a constant struggle with HD space.

I will keep organizing and tidying (sometimes it's relaxing and fun), but I will try to do the bare minimum just so that I'm able to find stuff again and not have it too messy. I need to spend the time enjoying the content rather than just organizing forever.