Glide64 or Jabo's D3D8 work best with this game, but:
- If you don't have a Voodoo card (almost certain since they have no longer produced) you need to use a Glide wrapper for Glide64. The Glide Wrappers have limitations so that motion blur and hardware framebuffer do not work, so pretty much makes it comparable to other plugins that do not support the game as well. Glide64 on a Voodoo 4/5 card displays everything correctly in Majora's Mask to my knowledge including day transistions and motion blur.
- Jabo's D3D8 can display everything correctly apart from day transistions, which are almost emulated but junk appears in the border. Jabo's D3D8 requires a graphics card with pixel shaders for everything to work as it should. If you don't you'll get various glitches.
If your graphics card is not a Voodoo card or a card that supports pixel shaders, you are left with Jabo's D3D6, Rice's Video, TR64 OpenGL (these don't support the motion blur or no day transistions properly), or glN64() (requires graphics supporting OpenGL 1.3+ I believe).
So if you can't use Glide64 natively or Jabo's D3D, you'll get a lot of problems that will be unsolvable that you'll have to live with.