Youtube? Nope. Any other site with videos? Nope. Only WoW (World of Warcraft) gives me beautiful sound. Whyfore? This only happened recently.
Firstly, some system specs would be helpful. Read relevant the stickies at the top of GQ.
Secondly, open up your sound controls (Control Panel on Windows, System Preferences on OSX, etc) and tell us what settings you see there.
Are these USB based gaming type headphones or regular audio mini plug? If USB you typically have to install and configure an audio driver for them to work with regular audio. I think WOW may have the USB interface built in.
I’ve found that in a 5.1 or 7.1 setup, flash only uses the front speakers for some reason. Perhaps your headphone jack has been redesignated as side or rear speakers somehow? I’m afraid I’d have no idea how to change it back if that’s that case.