I have a thread rack but most of my thread is stored in plastic see-through boxes. I have it sorted into cotton, poly and embroidery thread. Then there are the bobbin holders with different colours for the different threads. I also put a dab of nail polish on the bobbins so I can tell if it is cotton or poly thread.
My machine needles are sorted on a tomato pin cushion, it is divided up so I know where the different needles are.