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.