I do not know about all formats, but colors replacement (Ctrl-U, Transformations/Image/Replace color) does not work for 24bit BMP at least.
It works fine for 8bit BMP:
before: http://prboom-plus.sf.net/8bit_before.bmp
after: http://prboom-plus.sf.net/8bit_after.bmp
For 24bit BMP it does replacement only in first column:
before: http://prboom-plus.sf.net/24bit_before.bmp
after: http://prboom-plus.sf.net/24bit_after.bmp
