Rumor has it that body was discovered at around 17.00 and birthday reception was at 18.00 with Putin not showing up, so if you think that it was Putin, he personally does not seem to have alibi.

As for cuo bono, theories seem to be, in order of significance:

 o Kadyrov (last Politkovskaya's investigation was into where Chechnya reconstruction money are going);
 o enemies of Kadyrov (as he is the one most likely to benefit);
 o Nevzlyn or Berezovsky (provocation and misguided attempt to create Gongadze-II);
 o "concerned" citizen (Politkovskaya was not an exactly popular journalist);

Putin does not come up, primarily because he personally is not threatened at all by Politkovskaya.