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This issue was brought to my attention earlier today: the validator does not seem to do any integrity checking on attributes that specify color. As a very simple example, consider the tag: <body bgcolor="#CC0000"> This is perfectly normal and validates fine. Now consider: <body bgcolor="#CC00"> This is apparently invalid. In fact, Mozilla browsers will not accept this tag and will render white. This was brought to my attention when a beginning webmaster asked my why his backgrounds only worked in IE. My first reaction was to tell him to use the validator to check his code. To my dismay I realized that the validator passed the above short tag with flying colors, no pun intended. I'm not sure how the actual HTML specification regards this issue, or how far in depth the validation should go, but I think merely adding a regex to check for the # followed by 6 chars would be a big help.
Yes, the Validator will only check for constraints spelled out in the DTD of the relevant format. We are working on solutions to this problem. In the meantime you might want to try tools like HTML Tidy or http://schneegans.de/sv/ which should be better at complaining about such problems.