Try jabos plugin may have some gfx issues though,also give rice's video plugin a try,if those don't work well check out the plugins section and get more gfx plugins.
OK, for zelda you should try glN64 or Direct64.
For Perfect Dark use the latest version of Glide64 and the included glide wrapper (glide3x.dll). Don't forget to place the file named "glide3x.dll" in the directory of the emulator.
If you experience problems with the above plugins use Jabo's GFX 1.5.1 or Rice's video 5.6.0.
You can get all of the above plugins from the dowloads section