Skim has a "feature" that drives me insane: a large preview tooltip when the cursor is hovering over any link within the document or in the Table of Contents.

Instinctively, I'll move the pointer along the table of content to hold my place and this giant (relatively) image hovers over a large portion of the list I'm trying to browse through.

(The screenshot made the tooltips partly transparent, and not as annoying as they are in reality). Fortunately there's a hidden preference you can change using defaults. Do this:

defaults write net.sourceforge.skim-app.skim SKDisableTableToolTips 1

The wiki page that documents this has a bunch of other interesting settings on the page as well.

This may have been my unfamiliarity with using defaults, but the default type for boolean is 0/1. If you wish to use "true/false" or "yes/no", you need to explicitly pass -type boolean.

Also, I couldn't get defaults to find the app using just "Skim", but your results may vary and the invocation above works just fine.