So as the title says, which one would you choose? It would be great if one can also explain the reasons behind.
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FreeGLUT is a simplicistic framework for the creation of small OpenGL demos. Alternatives to FreeGLUT would be SDL, GLFW, or full blown frameworks like Qt.
Mesa is a open source implementation of the OpenGL API, and together with the DRI/DRM project drivers forms a full HW accelerated OpenGL implementation. If you're using Linux and use your GPU with open source drivers, Mesa is the OpenGL implementation you use. That's not a choice, that's a fact.
They're completely different things and neither can replace the other.

datenwolf
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Seems like Mesa *does* [provide](ftp://ftp.freedesktop.org/pub/mesa/glut/) a GLUT implementation, at least for GLX and Win32. – genpfault Jan 31 '13 at 19:52
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2@genpfault: I wasn't aware of that. But this is called MesaGLUT then. – datenwolf Jan 31 '13 at 19:53