You could put a - before the games you like the most. For example if I wanted Pokemon at the top I'd name it "-Pokemon Soul Silver".
That's what I do as well.
To the OP, if you're using AKAIO, you can also make a shortcut to a game of your choice and put that on the AKAIO desktop/root folder. I do that for the current game I'm playing the most, so I can start the game up very quickly without going through my folders. Just select a rom title and press "Y" to get the menu and select the create shortcut option.