Shadows of the Empire works near-perfectly in Project 64. The problem is that the default settings are wrong. You have to make sure the Counter Factor is set to 2, not 1, and the VI Refresh Rate is at 1500, not 2200.
Just these two settings alone will fix a great many games that were broken in the more recent revisions. There are only a few that actually need them the other way. You also need to make sure you’re using Glide64 for your video plugin, because the default plugin is riddled with graphics glitches. Turn on ‘hardware frame buffer emulation’ and ‘software depth buffer rendering’ to enable many effects in various games that would otherwise be shown incorrectly or not at all.
Having said that, I’ve become increasingly dissatisfied with the state of Nintendo 64 emulation, since it still has many errors and shortcomings that get in the way, and don’t look to be fixed any time soon. Because of that, I’ll be using it less in the future, and spending more time on the actual console. The biggest problem with this is the joysticks are so prone to wearing out, so I’ve been looking into ways to repair or replace them. I got one of the ‘Gamecube-style’ sticks, which are very well made and won’t wear out, but since the sensitivity on those is completely screwed up and it’s really hard to aim properly in GoldenEye with it, I ordered a custom circuit board from a guy in Germany which is designed to fix the sensitivity and make it respond much more like a new original. I’ll have to learn to solder in order to install it, but it’s very much worth the effort.
On the subject of Zelda—if you’re going to play Ocarina of Time, for god’s sake, make sure you get a copy that is either version 1.0 or 1.1. Version 1.2 introduced the absolutely horrible revision to the music in the Fire Temple, which eliminated the awesome chanting and replaced it with some generic rubbish that just doesn’t fit. Listen to the original here: https://www.youtube.com/watch?v=VwGVb8Ivb9E