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Other than that, I can't think of any warning signs. Also, appreciate that every drop in ranking is not a true penalty, in Google's terms. Some webmasters are rather casual about using the word penalty for almost any drop in ranking, when in many cases, it could just be a change in the algorithm.
Also, the penalty came in two steps. It was something like a loss of 25% for a month or so, then a loss of another 25% for two months, followed by (after numerous changes to make every conceivable aspect of the site squeaky clean) a recovery to previous traffic levels.
For the penalties which he doesn't hint at weeks if not months in advance, he sometimes explains afterwards.
Don't expect too much before/after. It can be very vague, but, hey, it's better than nothing.
Matt Cutts = The Prophet of Doom
(for those who don't listen to him).