I was wondering if there was a way to fix some of the graphics in some of the n64 roms ive got...

Now I know that there is no such thing as a perfect rom but when I was playing Mario party 3 on my
project 64 emulator some of the graphic are Skewed into one corner which screws up some of the mini games
thus making the game less enjoyable...

Is there something i can do to remedy this or is that just the way its gunna be?

Or should I go to the project64 web site and download updates or sumthin...

Not much besides trying different plugins and make sure you have the newest version. N64 emulation is still FAR from perfect.