So you're approaching this wrong, slightly. It is all emulator based, not an external system.
So for the example of RetroArch you get that set up then when you load a core and a game you can edit Shader options in RA. Desmume and PPSSPP have them too for example but they also have scaling options mostly which is not necessarily the same as internal resolution scaling, but close. RetroArch does Internal Resolution scaling based on the core you have loaded, so the DS Core does this. Then there is shader's for various set up's based on the system you are emulating (the Pixellate shader doesn't work great with 3D games for example), and then there really isn't scaling options except for the resolution of the window.
So if you are trying to get Shaders for SNES, etc, watch our Tutorial series on YouTube. The link is in my signature. Most tutorials deal with RetroArch but not at all do I talk about shaders, only some.