Most stock apps will use the proxy settings, but apps from the App Store rarely use the proxy settings given under Settings > Wifi. I am told that the proxy API must be called explicitly, but is there a way, perhaps a jailbreak app, that will force all connections to go through the proxy? I currently have the option of using either a .PAC config file or typing out the http proxy of my university manually and providing authentication details.
I was able to proxy URL requests from 4 apps I just tested (Instagram, App Store, Omni Focus, Bookmarks). I used a manual proxy configuration and Charles to test.
I'm not sure what proxy API you're talking about. From personal experience, I know that any app using an NSURLConnection to make the request will go through the proxy as defined by the system. It's possible some apps use a socket directly to make the request - if so that may bypass the system's proxy settings, but I'm not sure about that.