Boxes, jars and bags may be used to store less valuable coins but are not generally adequate for more valuable coins. There are specially made coin storage envelops made from acid free paper that hold a single individual coin provide a suitable and cheap storage method for most coins.
Plastic re-sealable bags or "flips" is a good storage choice because they let you see the coin without removing it from the cover. Mylar-lined cardboard sleeves (usually 2"x2") are similar to plastic flips and are a good way to store and package coins for shipment. Cardboard or plastic coin albums are great for storing a series of coins related to a particular country or theme.
Tubes are plastic containers good for storing several inexpensive coins of the same size together. Very valuable coins are often "slabbed" or encased in hard plastic holders as this offers the greatest protection of any storage method.
A couple of things to remember with storage: If you live in a very humid area add some silica gel to your storage container and keep your coins in their storage containers in a secure place such as a safe or fireproof box.