|It happens with The Legend of Sun Knight. It's a really funny and interesting series, I highly recommend it. But the releases are slow, so I recommend The Legend of Sun Knight (Novel), as it updates much faster and is even funnier.
Gong Hua (Novel) - not many chapters yet, but from the summary, it seems like this kind of route.
Hoshi no Samidare - as far as I've read.
Durarara!! (Novel) - the anime is also great. Not sure about the manga.
Spoiler (mouse over to view)
Though, it's not so much turning to dark, more like they seem "light" but are revealed to actually be dark.
Yu Yu Hakusho - later on in the series.
Black Lagoon - pretty good.
School Days - yup.