Yoshi Story Fix inside, if you're one of the people having problems with it.

Use Jabu's Direct3D6 1.5.2 plugin. Enable the advanced features. Force Normal Blending. PJ64 v1.6

Bamf. Perfect Yoshi's Story Emulation. No crashes. No blackscreens. No graphical gliches. Nothing except a game mind-numbing enough to make your brain leak out your ears.