I have a folder on my desktop where all my current projects live, and every new project goes into one of three folders: Practice (song recreations, practice with new plugins, and practice from textbooks/guides/tutorials), Random (sound design experiments, weird self-challenges, shit like that), and Sketches (everything else).
If I think a song has a lot of promise, I put it in another folder called Finish Me, and anything that doesn't feel like it has much potential goes onto a "Sketchbook" folder on my external hard drive so I can take bits and pieces from it later or come back in X months and see if I have a new idea for it. Anything that I finish goes into a completed projects folder on my external.
With regards to sample libraries, I divide things up based on whether they're of dubious legality (given to me by other people or containing copyrighted samples), free samples from online, or purchased royalty free music. I used to sort all the samples I purchased into their own categories, but now I just keep them inside their original sample packs so I can keep track of where they're from.