I have a wide variety of different sized/shaped containers like the ones shown above to keep all my loose bits in, but lately I've taken a serious shining to the smaller sized boxes sold by Really Useful Boxes:
http://www.reallyusefulproducts.co.uk/usa/html/onlineshop/rub_craft.php
They're good for storing stuff that "goes together" like all the bits you have reserved for a specific conversion, or all the bits from a single kit that you haven't been able to put together yet.
They're a
UK-based company, from what I know. And although I only own their simplest box types to this point, they do seem to offer a variety of compartmentalized boxes for all your grab-bag bits that don't have a specific future outlined for them at the time of storage.