Just tried out "Spider-Man - Return of the Sinister Six (U)" on 0.5.3 and the graphics are, well, out of place. 
I even tried the Extend Vertical Blank by one scanline but that didn't fix it. Here's some screenshots, one of the bug in Jnes and the other of how it's supposed to look in Nestopia:
I even tried the Extend Vertical Blank by one scanline but that didn't fix it. Here's some screenshots, one of the bug in Jnes and the other of how it's supposed to look in Nestopia: