Depends on your video card primarily, and which game you are playing.
- Glide64 probably supports the most games with fewer graphical glitches right now. It supports motion blur, hardware framebuffer, and dithered alpha among others.
- Jabo's D3D8 1.6 works well with most of the popular games and has slightly lower requirements.
- Rice's Video/Glide64 can use Hi-resolution texture replacements. Rice's Video is required to play a handful of games properly and at a playable frame rate.
- Direct64 supports hardware framebuffer, dithered alpha and overscan simulation, and works well with the games it can support if you have a good enough video card.
- glN64() works very well with certain video cards that aren't so good with the other plugins that require pixel shaders.
- Jabo's D3D6 1.5.2 works well with old video cards and integrated graphics.