GNU Image Manipulation Program
How to remove pure white¶
Quote from Dalestan (http://www.tt-forums.net/viewtopic.php?p=805832#p805832):
Well, some. Open each image in GIMP. Use the Color Select tool (Shift-O), with the threshold set to zero, to select everything that's #FFFFFF. Use the Fuzzy Select tool (U), with the threshold set to zero again, to unselect the contiguous background block, and then use the Paint Bucket (Shift-B) tool to fill the entire selection with #FCFCFC.
This, in a couple minutes, fixes all internal whites, without concealing any warnings about sprites that include the background.
Then save, encode, and manually fix the remaining ones.