Let's not forget Grozny. The Russians leveled that city more than once, but it is still inhabited.

The only city I can think of is Pripyat, in the radiation exclusion zone around Chernobyl.

There must be any number of cities in the Russian interior that have declined considerably since Soviet times. Of course, none of these are megacities, which is the OP's interest.

Oh, certainly not a megacity, but Ajdabiya in Libya essentially emptied out completely due to the fighting there. Of course, once the dust settles, residents will likely return, I presume.

However, certain events in recent memory make me wonder how soon before we see a major city actually abondoned for one reason or another. If things had gone a bit differently, what might have happened in the short term or longer term with certain recent events. Events like Katrina and New Orleans, the recent Mississippi River flooding, Deepwater Horizon and the Gulf ecosystem, the surprise massive earthquake under Chrischurch, NZ, the earthquake, tsunami, and nuclear situation in Japan, etc.

Especially in Japan, what if the earthquake and tsunami had occurred closer to Tokyo? Or what if the prevailing winds from Fukushima Daiichi had blown radioactive particles southwest towards Tokyo most of the time instead of straight out to sea? This situation in particular really concerned me considering the size and importance of a megacity like Tokyo.