I actually did this one too (in the almost published until the publisher decided to work on his pirate book instead Dragon Claw Apocalypse) where the protagonist is either supposed to find a major villain or a godlike figure and in the midst of his travels, he comes across a wandering holy man, beggar monk, whatever. And then its only a matter of time before the hero finds out that - SHOCK!!! - the beggar monk is really the Evil Villain (or godlike figure).
catvalente just mentioned Bridge of Birds and I've just finished the first book in Jack Chalker's Lords of the Diamond series and I just realized how often this has been the major plot twist - so much so that it'd be a bigger plot twist if the damn beggar man, monk, whatever turned out to just be a damn monk instead of the SUPER SECRET LORD OF EVERYTHING.
Although now that I write it, I realize that it's been awhile since I've read this kind of book. I have kind of missed that cliche.