This is really difficult to pinpoint because there are good elements to even some of the earlier NuWho dalek stories. Unfortunately, yes there's a lot of shit in there too, but it's difficult to make a complete hash of the Daleks because there are certain qualities that can't be changed wholesale, otherwise they wouldn't be Daleks.
Having said that, Genesis is quite clearly a peak which would never be reached again, but I still think there are some redeeming qualities in many of the stories which came after.
Part of the problem in a way was tying the Daleks to Davros after Genesis, diminished them as force in their own right. Davros was such a brilliant character, but I felt it was a mistake to bring him back so soon, if at all. (although I've heard this was down to Terry Nation who owned the copyright on the Daleks, demanding that Davros be used in subsequent dalek stories?)
I actually think that Davies used the Daleks quite well as a rule. Yes, Dalek had those corny scenes, but they were at least attributable to just one lone dalek in a highly unusual circumstance. Plus when the Dalek managed to free itself it goes on a cold killing rampage that any dalek would've been proud of, and that emo ending and Rose guff aside, it's still arguably the best Dalek story in NuWho.
Similarly, there are legitimate complaints to be railed against some of the writing in the Parting of the Ways, but not much of the script inadequacies are really around the Daleks themselves.
Doomsday is certainly a contender, being little more than a fan wank battle between the two most famous Who enemies, but again the Daleks themselves are consistent.
So I've gone for Daleks in Manhattan, because whilst it's far from the best of Dalek stories, the fact that these are four isolated Daleks looking for a way to reboot the continuation of their race, does allow for the story idea to have its own internal logic, though obviously not without flaws. And as a story, it's actually rather better in many ways than its predecessor.
For me I think it's the horrendous S4 finale where the Daleks finally jump the shark. Although you could say that they've been gradually jumping it ever since Destiny of the Daleks.