Unless it is a quick use changeout (like sewing silk thread for a small project) then back to my regular wt, I also toss my machine needles out. I use empty plastic water bottles, preferably the small ones.
I store my new unused ones in their original packs. I do need a better way to hold those packs.
I had a class where the teacher suggested using one of those large tomato shaped pincushions. The tomato is "divided up" by lines and marked for quilting, microtex, etc, but I didn't like the method very well, since it wasn't going down to needle size, just type.
I have seen those magnetic needle holders that are sized like this one: Blue Feather myPad For Needles Machine Needle Organizer. I don't know how well they work.