The games aren't available directly through the Nintendo eStore, though. If you want to get them, you need to go into the eStore, then into the Menu, then into Other Settings, then into Redownload Games. The games will be added to the list of games you already downloaded to the 3DS, and if you have a big library, you might have to scroll down some.

Instead of downloading each game individually, you can save time by selecting "Download Later," which lets you queue up the games to download over SpotPass while you're doing other things. You still need to select each game, but it's a bit faster and much more convenient.

The games are:
Mario Kart: Super Circuit
F-Zero
Yoshi's Island: Super Mario Advance 3
Fire Emblem
WarioWare: Mega Microgames
Metroid Fusion
Kirby and the Amazing Mirror
Mario vs. Donkey Kong
The Legend of Zelda: Minish Cap
Wario Land 4