On Linux (and BSD) I tend to develop 3D (and 2D) games with the following configs
C++, freeglut, glew, gl, glm, png (for sound, openal, freealut, ogg, vorbis)
C++, SDL, glew, gl, glm, SDL_image (for sound SDL_mixer)
Both work great, and the latter can also use Emscripten to be compiled to Javascript (asm.js), WebGL and run on a web browser. Using lots of smaller tech like this rather than a single games engine makes it quite easy to port to Android, iOS and all the many different flavors of UNIX and Linux since you can swap out individual components (i.e inside #ifdefs).
If you would prefer a more complete solution, there are some pretty decent engines / renderers compatible with Linux too such as Irrlicht, Ogre, Horde, Panda3D (very good with python).
If you want to go the .NET route, there is OpenTK (OpenGL related tech wrapper) and MonoGame (XNA compatible API) (which is completely broken on FreeBSD and some of the more "stable" distros such as RedHat Enterprise 6).
Also, an interesting thing to do is run ldd on your favorite Linux / UNIX game and see what they technologies they use. i.e
$ ldd /usr/local/bin/quake3
$ ldd /usr/local/bin/nwn