Conventional wisdom is to rotate your stored water every 6 months unless it's in sterilized, sealed containers (Aquablox etc). Adding a drop of chlorine bleach per gallon is supposed to prevent bacteria growth too.

Nalgene bottles are great for camping but awfully expensive for storage, like $8-10 for a 1 liter bottle. For a 72 hour kit you want at least 12 liters per person just to survive, so it adds up fast. I haven't had any leakage problems with the clear-style gallon jugs. I'd stay away from those translucent milk jugs. The 7 gallon Reliance containers are also good.

Aquablox supposedly have a 5 year shelf life. They come in 8 oz and 1 liter sizes. I'd get the 1 liter. Again, though, this stuff is way more expensive than storing tap water or even buying retail bottled water. A case of Arrowhead bottled water (24x0.5 liters) is on sale for $4 at Rite-aid this week. Maybe I'll go pick up a couple of those.