First, when i am working a pattern that i am not making up from the top of my head (which happens alot when i crochet, i am new to knitting), i have the pattern put on a zip drive for my laptop. then i can have instant access at anytime. I get migraines from light sources (house lamps, car headlights, computer screens, etc), so i have low level lights in the house. but i can back highlight the lettering on the patterns (make the background black and the letters white) and have less problems, therefore able to do more work. other things about using a laptop for patterns is i can highlight special instructions or repeats, increase fonts when the pattern is very small, etc. plus it cuts out the paperwork and clutter in the livingroom! i keep hard copies in storage somewhere, but since i have backups for the computer, i never need them.
as someone said earlier, i also use the 1 and 2 gallon size zip loc bags for projects or even for storing yarn. i have pets and even tho they are supposed to not get near my projects, they are pets! i keep lint removers nearby and also lint-free cloths (towels) so if i am working on something for a baby or someone outside of family the items are never in contact with animal dander. boy do my cats love baby items!
i keep all buttons and decorations in a small tackle box, boxes sold in the craft section are too expensive!
i mark rounds with small (1/4 inch) remnants of yarn. everyone has snippets around!