Here are some settings for Conker's Bad Fur Day:
~mupen64plus.cfg

[Video-Rice] #This will fix the colored black tail and a few other things. Sometimes this setting isn't found in the cfg. #I think it loads only hi-res textures for when there are far away objects it would load lo-res. LoadHiResTextures = True #This will fix the transparency of the fence. NormalAlphaBlender = True

It might be possible to add these to the .ini files for the specific game. But I'm going to move on to other things for a while and probably won't get back to this. There are some settings that improve performance and I don't know exactly which ones these were, I could post my entire plugin configuration if someone wanted it. The setting for the dancing toadstools remains to be found, maybe I imagined it.

And here are two settings for Starcraft 64:
~mupen64plus.cfg

[Video-GLideN64] #The game fails without this, however it slows down the menus immeasurably. BackgroundsMode = 1 #FBinfo needed for scroll updates in-game, however the logos at the beginning are no longer able to be seen. DisableFBInfo = False