It seems that in D/P, pokemon managed to get cheerier and darker at the same time. On one hand, there' spiritomb, the pokemon that was sealed away into the odd keystone, sendoff springs, where the spirits of dead pokemon are supposed to go, and that tower by solaceon town, where you see a lot of tombstones and a couple of people mourning for their lost pokemon. (The lost tower seems to be a recurring element: there's the tower in Lavender city, there's probably some other tower in GSC, that mountain in the middle of route 122 where you get the orbs for RSE). On the other hand there's the random internet humor, the swimmers and lasses ranting about their bikinis and miniskirts, and the famous engrish line
"Regigigas can't get it going because of its slow start!"
Also, I'd have to agree that the manga is seriously dark.
(If you don't want manga spoilers, don't read the rest of this post)
Not sure about any of the D/P issues or the Battle Frontier volumes (serebii hasn't updated its manga section, and all that wikipedia's telling me is that Diamond and Pearl are two guys, acting as a comedy team and bodyguards for the female character), but I've read that team rocket fused together a flareon, vaporeon, and jolteon at one point, and the three legendary birds at another point (and you thought Mewtwo was bad?). Ruby and Sapphire almost get killed by mightyena and a seviper at the beginning of their series, and at the end of the FR/LG saga, Red, Blue, Yellow, Green and Silver get turned to stone after Mewtwo tries to keep Storc from capturing Deoxys. There's probably a lot that I missed along the line, but I'm reasonably certain that this, combined with what mastadi said, nominates the manga for "Darkest part of Pokemon."