At the moment, if you download something from the DSiWare store (downloadable games/programs for the DSi), the program will be linked to the DSi console you download it on, rather than to the account you downloaded it with. Whilst the reasoning behind Nintendo doing this seems to make sense (to prevent you from downloading the game onto all your friend's consoles, while only you pay for it), there is a bit of a bump in their plan - a new handheld shaped bump, known as the 3DS. If the current system stays in place, when DSi or DSiXL owners want to upgrade to a 3DS, they won't be able to bring their downloaded games (that they've paid for) along with them to the new console.
Luckily, Nintendo of America President Reggie Fils-Aime says that Nintendo are aware of this, but has said that "until we move to a different type of approach, like an account based approach, you're not going to be able to transfer the content".
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If you've purchased DSiWare off the DSi Shop, you'll only be able to play it on your DSi for the time being
With Nintendo's current online approach being rather behind when compared to the other companies (having to exchange friend codes unique for each game to play online, for example), an upgraded online service for Nintendo consoles has been long overdue.
Nintendo seem to have realised that people are tiring of the friend code method of multiplayer, with Pokémon Black and White allowing for random online matchmaking, so hopefully a new account based Nintendo online service isn't far away.
We just hope it's out before the 3DS is, or it could impair the sales of what could be the most successful handheld ever.
We'll have more details closer to the 3DS's launch, whenever that may be.