I'd venture to say even more than the "vast majority" lol, something like 99.999%, if it's not in app store or cydia it must be something really strange or extremely "shady", unless he's talking pirated apps.
I would assume you would want to use the app store as least as possible if you have a jailbroken phone or pirated apps, Apple is vigilant with that stuff, who knows what they might try to do to your phone once it's under itunes control.
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