One of the worries about the 3DS was whether the DSiWare that you'd lavished your hard-earned Nintendo Points on would make the jump across to the new console. According to a Nintendo PDF, the answer is "yes, but with limitations."
Those limitations seem to be that some software simply won't be transferable at all, though there were no indications of the games they might be. It could be a similar situation to transferring Wii save data, where games that utilise the WiFi Connection will be locked to the original DSi, but it's likely the vast majority of software will be available for transferring to the 3DS.
Although Nintendo didn't announce anything specific about 3DSWare, the same document did mention that downloaded software could be transferred from one 3DS to another, paving the way for a more robust system than is currently available for DSiWare.