Personally, I have several categories that I put my (X)HTML files themselves in that correspond to the website's topical hubs: like Creative, Thoughts/Blog, or Shrines.
These are folders and they contain the individual subfiles for pages they contain and their main hub pages. For instance, my Music shrine is under /shrines/music/main.xhtml, whereas the Shrines page itself is under /shrines/main.xhtml.
As for images, they're all in a /graphics/ folder with additional subfolders for /graphics/gifs/, /graphics/img/ and so on. I also have /scripts/.