I have almost completed Yoshi's Story in PJ64 and here are my observations from running it on my system:
1) It has the same sort of 'sprite' issues as Kirby, namely 3D objects go flat when they move.
2) The game often locks up PJ64. It feels like a memory leak or
something. For example i'll play for 30 minutes then the screen slows down, eventually goes white and the emu locks up. If i restart PJ64 and reload my savegame it runs fine again. The worst offenders were the cloud level and the jungle level.
3) Certain levels are unplayable. Noteably 2 of the levels on the 2nd page, the one with Blargo's Boiler room and the skeleton snake thing. I cant remember which. On one the platforms are semi-invisible/corrupt and on the other one they dont appear at all.
My spec: PIII933, 768Mb, Radeon 8500 (Cat2.1s), DX8.1, XP Pro, using D3D6 1.5 and all my roms are clean.