yup that can be annoying lol. well i read about this somewhere, n it worked great for me:
on ur sd card, create a folder called ringtones, and another one called notifications (if u need it) drag ur ringtones to these folders n they wont show up in ur music app.
the guy said u need to format ur sd card or it might not work, so i guess u should do that if u can. i did. although u dont mention if u have an sd card or not. im not sure how this works on the phone memory
yeah, the .nomedia file is great if u dont want any stock app to pick up particular media.. i.e. videos/sounds from games etc.