I've tried all three. I like 1964 for Goldeneye and Perfect Dark, for the 60hz and the Mouse Injector.
Project 64 is slow for me with "GlideN64". And "Glide64 final" doesn't detect it in 2.3 version. The included glide64 version doesn't have an option to configure 16:9. And also doesn't detect "MouseInjector.dll" any version, 1.6, 1.7 and 2.3