Do you have the free software called true sizer, by Wilcom it has an edit on it for just that.
www.wilcom.com.au/truesizer

Apart from deleting them or using your imagination and coming up with fantasy animals ;-) I really can't help. Seriously, I try to stitch them out in what I think would be nice colours and them look how I could improve them. I'm curious what truesizer could do!

I have the same problem. I've found that if I download small designs in PES and DST formats and compare the colors, I can use my imagination and fill in the colors in for the designs which have no color charts and are in "weird" colors. Even though you don't like embroidery.com, you might change the formats of the designs you have to DST at their web site and the colors will change back and you can compare them. CSD, EXP and DST seem to change the colors when converting to JEF, etc....