It is a not-so-secret secret that Photo Ninja installs and runs well under Linux .... if you aren't familiar with this RAW conversion program, you ought to be.
I'm in particular fond of PN's capabilities for handling my UV and IR captures.
RawTherapee is another program that comes in a Linux flavour. Like PN, it digests almost anything RAW-wise.
Aftershot by Corel does well under Linux, cannot remember whether it comes in a native Linux version, but that doesn't mattrer as long as it works. Aftershot hails from the old and beloved 'Bibble', unfortunately after Corel purchased it development has been on and off. Largely the latter if truth is to be told, thus support for the latest cameras is so-so.
I discovered by accident that Monochrome2DNG (which I use for my monochrome NEX-5N) runs perfectly under Linux as well.