[EDIT 18 Jan 2015: This has now been fixed in 3.49! Thanks to Richard Koch and company. Copied from http://pages.uoregon.edu/koch/texshop/version.html:
Three hidden preferences were added, allowing users to change the yellow highlight color to another color, when used by inverse sync from the pdf window to the source text. This is helpful if the user has changed the default colors of the source window. The new items are
defaults write TeXShop ReverseSyncRed 1.00
defaults write TeXShop ReverseSyncGreen 1.00
defaults write TeXShop ReverseSyncBlue 0.00
Inverse search in TeXShop, invoked by pressing the command key and clicking on the Preview window, jumps to the corresponding source. This is a great feature, but the text that I jump to is highlighted in a yellow color that is very difficult to see. Further, until I click in the source code window, any text I select (e.g. with shift + arrow keys) is also highlighted in the same hard-to-see color, as opposed to my system standard for highlighting (purple). This happens even though the focus is on the source window.
This seems to be a built in feature of TeXShop, with no corresponding preference. Is there any way to set the highlight color?
I'm on TeXShop 3.48.1, OSX 10.10.1.