I bought some NES games on the Wii that are also sold in the 3DS shop. Is it possible to transfer them from the Wii to the 3DS?
There is no transfer from the Wii to the 3DS for games. You can transfer your Mii from the Wii to the 3DS, but that is all. If you want the VC games you bought on your Wii to play on your 3DS, you are going to have to buy them again from the 3DS eshop.