The ideas of doing something good with fees isn't so bad. I just second that it be volunatary. Just programme a voluntary 0.001 %btc donation button into the next bitcoin client for doctors without borders, the red cross and or even religious human rights groups. Though I'm an atheist myself, I think they act (thanks to their ability to act) instead of having endless philosophical discussions that lead only to contemplating the world's problems.
Sorry for the off-topic drift.
I don't think having the standard client take extra fees, even voluntary ones, and direct them to a specific charity (or even non-specific or multiple chartities) is a good idea, for reasons others stated above.
However....
From what I can tell, I don't think there's anything preventing any given charity from taking the standard client, keeping the credits and license, slapping their logo/name on it, and including such a voluntary fee. I suppose it wouldn't even have to be the charity doing it... if someone knows a charity that accepts bitcoins, they could release the "Red Cross Bitcoin Client" or "United Way Bitcoin Client" themselves. Everyone could then be reminded of their favorite charity every time they spend bitcoins, and be prompted (regularly or randomly) to add the extra donation; or it could just be an extra field on the "Spend Coins" dialog box.
This would avoid a lot of the problems mentioned above, and still allow for the basic concept. Should make everyone moderately pleased, if not fully happy.