Mommo Design has a bunch of inspiration for girly reading nooks. These quiet corners contain fluffy pillows, rugs, cushions, usually a canopy, and of course lots of books. I think the idea is very cute and I'd love to do this for my daughter's room.
Puzzle storage - "Buy some legal size poly expandable envelopes. Remove the string and replace with Velcro circles. Place in a bin. My rule is one out at a time. The envelopes are easy enough for my two year old to open and clean up himself.