Is the gloss on iOS icons automatically applied? Clearly it isn't completely automatic, as many icons don't have a reflection, but is there some sort of checkbox when creating an app to determine whether the gloss is applied?
Yes, it is automatically applied by iOS. 

There is an option for iOS application developers to turn this off, called UIPrerenderedIcon. This is a value in the Applications Info.plist, that can be turned on and off (checking it would note that this is a pre-rendered icon, and to not apply the gloss).

You can read more details in the iOS Human Interface Guidelines.

Web Applications (as noted in Mathias's answer) also do have this reflection applied to them. You can override this by naming your file apple-touch-icon-precomposed.png. More information is also provided in the HIG for web clip icons.