One thing needs to be kept in mind concerning the recent Nemtsov murder: he was a politician way past his prime. His political weight was low even within the Russian opposition, which as a whole is extremely weak right now; for most people, this assassination is the first time they'll hear about Nemtsov in a year or more. Many even argue that Nemtsov was a "decorative" asset for Putin as a stable, familiar, relatively honest but powerless opposition figure.
In short, this makes no sense, sort of like murdering Ross Perot in the USA. For Putin, Nemtsov as a martyr is a far, far bigger problem than he ever was alive. If not within Russia itself, where most people seem to be baffled (again, Ross Perot assassination), then on the international diplomatic and mass media stage, where people can be easily convinced Nemtsov was killed because he "was a threat to Putin". Three years ago, Putin warned about this exact scenario. Who benefits? May be internal Russian opposition, Ukrainian government, American government, heck even islamic extremists - but Putin doesn't benefit, that's for sure. Make your own conclusions.