I have folders and subfolders, and this is how my bookmarks are arranged.

• essential
• fun and entertainment
  • boards (message boards)
  • clothes
  • lost (the show)
  • ontd olympics (old folder from the LJ community of the same name)
• geekery (mostly fandom stuff)
  • challenges and memes (fiction challenges and kink/fluff/angst memes)
  • stories (fan fiction)
    • avengers (comics/movieverse) (Marvel)
    • crossovers
    • danny phantom
    • doctor who
    • glee (this one got so big that I had to subdivide it)
      • gen
      • het
        • puck/rachel
        • finn/rachel
        • puck/quinn
        • sam/mercedes
      • slash
    • gossip girl
    • firefly
    • hunger games
    • inception
    • lost
    • misc
    • misfits
    • once upon a time
    • pirates (of the caribbean)
    • prison break
    • pushing daisies
    • recs
    • rpf
    • star trek (abramsverse) (the 2009 movie)
    • supernatural
    • vampire diaries
    • white collar
  • fan art
  • misc (meta, commentary)
  • rp (roleplaying games)
• helpful
  • research
  • writing
  • clothes
    • shopping
• layouts/overrides
  • tumblr
• misc
• pictures
• school
• to download