Completely by chance I discovered that Texshop will let you encode the encoding of your source file in a comment, overriding the editor's default input encoding. For example:
% !TEX encoding = latin1
I knew already about the root command (% !TEX root = ...), which sets the main document for multi-file projects. By and by I also found out about the custom "tag" feature: If you add a line like
%: tag name
in the source, Texshop will include tag name in the "Tags" menu (available at the top of the document, not in the Menu bar), which allows you to easily jump to the location.
What other such commands are available? The "Tips and tricks" document (available via the Texshop help menu) mentions a few more in passing, but is clearly incomplete since encoding is not mentioned.
