I know that this question was asked two years ago. And I know that Andrew Fawcett has made something about this issue. Maybe anything has changed since then and there is a solution that find unused methods in apex and maybe furthermore in Visualforce?
If you download Mavensmate (compatible with SublimeText or Atom) there's a feature called Health Check which does this. The documentation is poor but it should be under Project > Health Check
If I'm inspecting a single method
I use the "Find Usages" functionality within IntelliJ's plugin called Illuminated Cloud. The downside to this is that Illuminated Cloud is not free, but it certainly does a bang up job.
If you do choose to use Illuminated Cloud you can use this functionality by right clicking on any variable, property, method, or class name and choosing "Find Usages."
Inspecting an entire codebase
I have had some good luck with configuring rules with SonarQube in the past to do health checks on entire code bases.