I'm using all of them in my project, as this seems to be the direction Microsoft is taking as well:

- Nuget for serverside .net (.cs, .dll) and msbuild (.target) dependencies

- npm for javascript development dependencies (grunt/gulp)

- bower for clientside dependencies (.less/.scss, .js)

I'm using the new VS online build stuff as well. In git, none of the dependencies are checked in. So the build starts with npm install, bower install and nuget / restore, then it runs gulp and finally msbuild.

I'm pretty happy with it.