Once you've moved them from the TamaTown web site, onto your Tamagotchi toy (by using the Logout password), you can use them to pay for items in the shop on the Tamagotchi toy, or items you buy from the TamaTown web site.
You can also donate them to the king. (Activate the book icon on your Tamagtchi toy, then select Points from the menu.) After you give him enough, the king will reward you with special souvenirs.