what about a 'main menu' where sub-icons are hidden, like
emulators
native apps
documents
utils
which you'd scroll down & up and then press right to get
emulators > nes > snes > gameboy > pcengine
native apps
documents
utils
then when you click the joystick you get the list of files/roms/whatever (on a new, clear screen or even something nifty like transparent over the previous screen which is now frozen, my point is, it's a new list like you currently have), which you again scroll up/down, and a left gets you back to the main menu.
i'm was thinking something very tivo-ish in case it's not obvious. the tivo menus are fun and addictive. *foop* *ping* *eep eep* *foop*