PNG images can contain a bKGD chunk which defines a background color; this is used for instance by Internet Explorer 6.0 when displaying PNGs with multiple-bit alpha transparency.
When we resize PNGs with ImageMagick, we specify a white background color, which is usually an acceptable fallback for decent display in IE 6 and generic image viewers. When resizing with GD, no background color gets set. IE 6 ends up displaying its generic ugly bluish grayish background, which is fairly unattractive.
Unfortunately the GD library doesn't appear to provide any interface for setting the background color. It might be relatively easy to hack up the file after saving, though, and add a hardcoded background chunk. :)
Just a minor thing, but it's these little things that keep people happy.