[Otaku]

If it is supposed to be subtle, I'd probably be looking at a Divine or Pact limitation on various, non-overt Advantages. Luck based Advantages have been mentioned, probably with an additional Limitation to aspect the Luck to a particular gods' sphere of influence. There are plenty of subtle things like Intuition, Danger Sense and even perhaps Talents (unless there's a rule against that =P) which could easily demonstrate how a god has favored a particular follower.

Many mundane Advantages work as well; something like Very Fit (especially if allowed under circumstances where it normally wouldn't), mundane Resistances, etc. all make sense for a god to bestow upon the faithful if it can be justified as a part of that god's domain. I mean, keeping your followers healthy and helping them live longer isn't flashy but it seems like a good way to grow your worshiper base not just by giving a benefit, but giving a practical one ("Followers of the god of health seem to live longer, heal a bit faster, have more energy, take ill less often and be a bit more virile than others", at least while they perform the rites that demonstrate their dedication to their god.").

Heroic Feats don't have to be flashy, do they? I mean if periodically someone seemed far healthier, better coordinated or stronger than they look but only for at most 18 seconds, if you aren't trying to be flashy with it, it won't be obvious. I mean, even from a metagame perspective a lot of what you could accomplish with Heroic Feats you also could accomplish by simply being fortunate in real life with your die rolls.