No$Zoomer 2.3.0.2 [there might be already newer versions] is using DirectX and it can be played in anaglyph with old iz3d software. And it looks awesome. [Win 7 x64]
It was hard to find on the web information about anaglyph support for ds emulation, or another stereoscopic support. I've also tried to find OpenGL Anaglyph drivers and discovered that Nvidia closed their Anaglyph support for all notebooks and after that I began to dig in versions of different emu that I loaded from Emucr.
Have checked them one after another, with iz3d and Tridef, and finally get to WinDS Pro - that is exactly a pack of nintendo pocket emulators. And there among other emulators was No$Zoomer emulator
just very happy now and finally will sleep calm.
Very big thanks to those developers who made the opportunity of anaglyph output for ds come true. They are Rock! *__*
[registered and posted here because it's the first page of results from Google search for any query tied to anaglyph/stereoscopy/ nintendo_ds emulator/desmume/nosgba. I'm sure this will help other people who are searching. Because I feel lucky that I found it.]
upd:
Iz3D can be combined with Nvidia Vision, making another great anaglyph output [for nvidia and external monitor only]