To keep an organized pantry, take the time while everything is out to wipe down the shelves and sweep away the dust and dirt.
The important part to the organized pantry is to group all those loose items together so you can find them easily.
Glass is a good choice for food safety, as sometimes plastics leach into the food. But if you have litle ones in the house who might break some of your containers, you might want to stick with plastic.