When I was running LyX 1.6.x, I had no problems getting LyX and Skim to sync, but I can't get it working with LyX 2.0.6.
No matter what I do, generated pdfs continue to open in Preview rather than Skim. LyX has the correct (according to the wiki) command built-in - open LyX Preferences -> Output and in PDF command put /Applications/Skim.app/Contents/SharedSupport/displayline $$n $$o $$t. And in Document -> Settings enable Synchronize with Output (I've saved that as default for all my documents). I'm generating pdfs with PDF (XeTeX) for the most of my test documents, as that is what I usually use, but I also tried a document with PDF (pdflatex). I'm running LyX 2.0.6, Skim 1.4.7 and MacTeX 2013 (which I updated about a week ago) on OS X 10.8.5 (Mountain Lion). Skim.app is in /Applications. I've also made the appropriate settings in Skim, but I need to get LyX -> Skim sync going before I worry about the reverse. I've looked in the LyX bug trac, this mailing list and also the macosx-tex (TeX on Mac OS X) mailing list. I seem to be doing things correctly. I know I could force the pdfs to open in Skim by setting all pdfs to open in Skim, but I neither want nor should have to do that. Any suggestions for troubleshooting this? -- Rich