Since the default background color on Chemistry.SX is white, any image, whether it has an alpha-channel to it (e.g. PNG with transparency enabled) or not (e.g. JPEG of GIF) looks fine.
However, quoted blocks (second layer of abstraction) have a different color ("Floral White" on main site, and "Solitude" on Meta). Dropping an image with a white background there creates third layer of abstraction, making it look like the image is not the part of the quote, but rather that they belong to the main text (since it also has white background).
Compare these two 2D and 3D graphics for the DAMN molecule:
To my eyes version with no background looks more superior in terms of visual appearance and layout. Technically there is virtually no difficulties in switching between both representations back and forth; however I think that preparing the graphics in PNG format with transparent background should be preferred.
What do you think, is it a reasonable suggestion, or just some bells and whistles?