you explicitly put stuff when you may or are installing software that "can " use other software..
example. if you know you are going ot install Mythtv then when you do the system you woudl put mysql in the use flag.
this way when qt is emerged it will put hte connectors for Mysql and mythtv uses thosse connectors. some times you have to reemerge when you do find something.
for me its was transcodeing.. I never put libdvdnav in my use and transcode keeped giving me an error that It could not read the dvd. so I did USE="libdvdnav" emerge transcode
for dvd burning software its always best to have dvdr in your use flag..