Insignificant whitespace and formatting markup
At first you might think, "well, whitespace is just a text node, and that's always significant." There are two problems with this. First, in many languages whitespace isn't that significant (XHTML, MathML, SVG, RDF, etc.) - browsers could care less. Second, there's whitespace which isn't part of a DOM node: the spacing between attributes. Case in point:
<author firstName="Isaac" lastName="Asimov" title="Dr."/>
Few XMLSerializer's will care about that, but it's a source of pain when dealing with revision control.
Does anyone know of any algorithms or existing API's for dealing with this adequately? I'm likely to write my own, but I would appreciate seeing whatever others have come up with.