Zip Lock bags are my favorite for all the bolts, etc. I write "bell housing bolts" on one, "intake bolts" on another, etc. I use a sharpie permanent marker to label them.

I also keep a notepad there, and make drawings of what went where. It's funny how you forget a simple thing like how the cam ecentric goes 6 months after you tore the engine apart. Notes make it much easier when assembly time comes.

I also "borrowed" some 2 litre coke trays from the local 7-11, they are made of plastic, and hold 8 pistons and rods perfectly, upside down.