A rolodex might be helpful for the really tiny parts. Perhaps in conjunction with microsleeves. Taping sleeves and/or cut tape to index cards large enough to stick or print a label on the card.
One of the most useful and versatile things for odd parts in my shop is a heat sealer and the foil bags that dig/mouser send many of my components in. I save a few, here and there, and have a small stockpile. You can make your own mini-sleeves with this type of bag which is very smooth and durable (against crinkles and whatnot). And you can make larger pockets right next to the sleeves to fully encapsulate labels which will never wear off and become unreadable. Even without the cut tape, you might have occasion to store small amount of parts or IC, and if they are rectangularish, you can make a custom minisleeve that will keep them neatly stored. Seal the ends of the minisleeve closed with a dab of your soldering iron. Cut them open with a craft knife and push as many parts out from the other end with a wooden qtip. Reseal. When empty, you have the all important label and part number if you need to reorder them.
As for failure... this can be a concern to these tiny parts. The foil bags are all very, very tough. A sealed foil, antistatic bag is akin to fort knox for small parts. These bags don't rip or tear or stretch or puncture without working at it. You could put a pound of small parts in there and throw it in a bin with 100 other different bags, and no worries of a bag failure.
For things I use regularly in higher volume, I find test tube rack and a funnel are handy for access. And I use small stackable, shallow dishes for holding the parts while in active use. I have 6 little dishes, which for manual assembly of my current boards seems to be enough unique parts to tackle at once. I write what the part is in sharpie on the edge and bottom of the dish and wipe it off when I'm done with the part and have poured them back into the test tube.