Hmm. For me, I found Project64 version 1.4 to work the best, and set it to RGB emulation if you want to get everything. It goes really slow that way, but it lets you see everything properly. And other than taking screenshots, I don't know of any other way to get the sprites. Are you trying to get still sprites, animated ones, or what? Because I have almost all of the still ones (and single frames from animations) and you can either get them from the Mariopedia or from me, already chopped out from the background and everything. So, I have to go now, but let me know if I can be of any further assistance.
"Thus has it ever been! Thus shall it ever be!"