save skim annotated pdf as pdf with annotations
Skim doesn't save notes and highlights within the PDF file itself. That's why they don't show up in other viewers (much like 'bookmarks' in Preview).

It's possible to export a copy with notes and highlights embedded: File &gt; Export… then choose file format "PDF" and mark the option "With embedded notes". They will show up in Preview and Acrobat. However, Skim can't edit the notes of the exported copy anymore. Apparently, Preview and Acrobat can, though.

Skim FAQ at https://sourceforge.net/p/skim-app/wiki/FAQ/

(based on Skim version 1.4.18, OS X 10.7.5, Acrobat Pro XI)