I am running the Adammer ADA Compliant skin on my sites to fill any State and Federal mandates.  In validating one of the external sites I came across issues causing a fail.  Adammer gave me the following information.

2) Error: the name and VI delimiter can be omitted from an attribute specification only if SHORTTAG YES is specified

This is caused by the poorly written Links module. The code should read <|td nowrap="nowrap"|> not <|td nowrap|>. The skin cannot change poorly written module code. Either way nowrap is depreciated and should be accomplished with a CSS style attribute like style="white-space:nowrap;". We recommend that you use the HTML/Text module instead of the Links module. 

Having my users edit/add links through the html/text module rather then the links module is not in the game plan.  I can see information being deleted etc...  Can this be corrected?  Or does anyone know of a third party links module which would pass validation?  Thanks. 
 

version 4.0.0 of the module will solve this (version has been submitted to the release tracker).

also: DNN 5.0 will be almost completely xhtml compliant

one of the things you could do is to check out the DNN 5.0 roadmap, and see what issues have been fixed that have to do with Compliancy: http://support.dotnetnuke.com/project/RoadMap.aspx?PROJID=2

I would very much like to discourage you to make changes to the core, as you will loose all those changes with an upgrade (eg. dnn 4.8.4 was just released, with a few security fixes....)

One of the things i did before was to use a third party http handler that could fix dnn output before it was send to the client. Check out Snapsis Pageblaster, that has a functionality to make the output xhtml compliant...