On the DS, I have a GBA/DS/SNES/etc. etc. game folder, and the few homebrew I have I keep either on the root for easy access or because it doesn't seem to work if it's in a folder. I don't have any music/video on my DS anymore now that I have my PSP.
On my comp, games are zipped individually and arranged the same except with a separate folder for backup DS saves in it's folder. I keep utility programs on an old 2 gig USB I keep in my DS case in the off chance I might want 'em when I'm elsewhere.
I rename shit to Name (E/Eu/J/Je/Ej).whatev depending on the language/region and whether it's a J game with a translation patch or an undub.