Do all Nikon's use battery packs?

I was looking to getting a Nikon, but it says that the Nikon D3100 and D5000 both use battery packs, are they really worth the trouble? Will I not be able to use my own batteries if the pack happens to go dead?

Battery packs give you more power for a longer period of time. They can last a year or two.

Li-Ion battery packs are by far the cheapest way to power a camera. They can be re-charged virtually for free and are cheap to buy, about the cost of a couple of sets of AA batteries so carrying a spare or two is not going to break the bank.
Pentax still use AA batteries on their entry level DSLR's, but even here your much better off using rechargeable, though they can use alkaline AA in a pinch, but they won't last anything like as long as a Eneloop rechargeable which they are designed to take.

I think they are worth the trouble. You won't really be able to use your own batteries with those models. However If you get a Grip for the D90/D80/D200/D7000/D300/D300s/D700 etc you can use Double A batteries with your camera which is really cool…

Those are Li-ion batteries which is the cream of the crop these days. They last the longest. You could buy an extra set of batteries if you are a heavy user. I've even seen a battery pack adapter that uses AA batteries but I'm not sure about it's efficiency.