I find that Skim and EF work great together: I convert my pdf to pdfd bundles, then when I annotate and save, all the annotations appear in EF.
One other great feature is that if I search for some text that is in an annotation, then EF accurately finds the records with this text.
There is one small drawback, though: if I use “Find” to figure out where the annotation is, I get a “Not found”. Hence (yet another) feature request: could Find also work on skim annotations?