Gilbert: That might explain why Mario is taller in Donkey Kong (arcade) than in Donkey Kong (ColecoVision and NES).
Another complicating factor is that a common PAR for home computers was 6:7 (Apple II, IBM CGA, and several others that used twice NTSC colorburst as the pixel clock) or even 3:4 (Commodore 64). If game graphics were drawn on one of these home computers, it might have affected the artist's conception of PAR. The only home computers I can think of that use NES-like PAR are the SC-3000 and MSX.
I plead guilty to not taking PAR into account in Thwaite. Explosions are a circle of radius 12 pixels, despite the 8:7 PAR of NTSC NES and the close to 11:8 PAR of PAL NES and Dendy. All I can offer in my defense is that assuming square pixels makes the collision detection simpler.
You can probably add every Super Game Boy-enhanced game too, as they usually don't have different sprites for Super NES play (8:7 PAR) from the sprites used on a Game Boy's square-pixel LCD panel.
Sprites looking wide and fat in general on a low-def console like the NES might just be
low-def super-deformity.