How can I change the Glossed app icon? Before iOS 7 on the iPhone, there was an option in settings to turn off the gloss on apps, how can I do so on iOS 7?
If you're talking about the icons on your home screen, as a user there is no option to remove the gloss. This is a developer feature. As a developer you uploaded a raw icon and (by default) apple would add the gloss. You could turn this off if you wanted to add your own gloss (to add your own other effects), or if you just didn't want the gloss at all. 

I've noticed that since going to iOS7, that MOST of the apps that had gloss, no longer do have gloss, but the occasional one does. This is obviously because the developer chose to add the gloss themselves and set the flag to have apple NOT add it. In this case, apple can't remove it.

Seems like apple thought ahead in this regard and it was simply a matter of turning this off to remove all glossed effects to match their new iOS. 

However, in the case that any developer added it manually, there will be no way for you to remove it short of changing the icon which just isn't possible.