Well, I have a somewhat different take on this than most people probably do. I am an analog aficionado first and foremost, and so if the CD does not sound at least as good as the LP version, than to me it can not qualify as a reference disk (whereas, the LP might). And since I much prefer the sound of analog versus digital, (even on most digital LP recordings to be honest), there are very few CDs that are duplicates of my LPs that would make this list. (So basically the only CDs that would have a chance to make my list are the ones that don't duplicate my LPs, and since I prefer the sound of analog anyway, those CD recordings are usually not my favorites, as I rarely listen to CDs because of my love of analog sound.) Therefore, out of the 1,000 or so CDs that I own, probably less than 2% would qualify.
So to answer your question .... maybe one or two dozen.
(But on a side note, I do like listening to the other 98% of CDs in the car!) :-)