Mike Wechsberg's review of my 1000 Control Amp in Positive Feedback Online Issue 37 has a good description of some of the advantages we enjoy using switching technologies in both the amplification and power supply subsystems. Here is the link, see the third paragraph:
http://www.positive-feedback.com/Issue37/acg_1000.htm
As to the "Does anyone have an experience with a particular Class D amp that bettered a reference quality amp?" question. Of course the quote I like best from Wechsberg's review is this:
"Probably the best characteristic of this amplifier is its ability to communicate drama and emotion in all the types of music I tried. So many other amplifiers are very good at reproducing what is in the record groove (or the "pits" if it's a CD) without really communicating the message. My current reference amplifier, the Krell KAV-2500 is more of a "reproducer" whereas the ACG is more of a "communicator." Given a choice I would go with the "communicator" every time."
One can find both reviewers and listeners on the web and in print who have retired 'reference' amps in favor of class D amps. The good ones have a transparency which is startling. On the other side we hear others who are essentially dogmatic in opposing the new type. My suggestion is to listen for yourself and see how your music and system react.