People can download games through the Nintendo eShop or by purchasing redeemable codes at retailers (in North America, Gamestop currently offers downloadable codes for Super Mario Land 2: 6 Golden Coins, Pushmo, and 3D Classics: Kid Icarus). Downloaded games will be saved onto SD cards, and the saved data cannot be shared with other systems. Retailers will be free to set the price of digital product they have in stock.
Nintendo plans on keeping the price of downloadable games about the same as their retail counterparts. This is totally different from other competitors like Sony whose pricing of digital games are marked down a bit.