Most latitude and longitude coordinates are defined relative to the WGS-84 standard, including GPS coordinates from your receiver. However, some coordinates are specified using local datums, and these datums are often imprecise enough that even if you did convert them to the same datum as your GPS receiver, your receiver would be over a hundred feet off. (Code 7700 has more information on the issue).
Some examples can be found through Jeppesen and Garmin, like some of the SIDs around WIII and approaches at FLKK. I don't have firsthand experience with any non-compliant navaids personally though so it's hard to tell how big a problem this really is.
Nowadays most (95%+) of navaids and airports are compliant. I've heard even all international Russian airports are now compliant. So what's the busiest airport with non-standard coordinates?