Go to that 3DS Guide, go to GodMode9 Usage, scroll down to Dumping a Title. It should tell you how. You can look up the title ID on that 3ds titlekey site, or just launch FBI, go to Titles, select the game, and you should be able to see the title ID for the game on the top screen.
I should have clarified: 3DS titlekey site does NOT include DSiWare title numbers.
In any case, I appear to have found all 10 of my installed DSiWare games, though they're in a diff place than the GodMode9 usage guide implies: SYSNAND TWLN/title/000300004. You also can't get title info for the games before you back them up. Dumping them as CIAs appears to work, but when dumped via the GodMode9 guide's instructions, they do not come with their title or listing images attached, which is funky. There has to be a better way to do this, right?
Basically, DSiWare works in a slightly different way in terms of backing up your own files, and none of the guides reflect this. Since DSiWare can no longer be re-downloaded via eShop, I'm trying to figure out exactly how to back these up.