+1 on the Font/Indent name.  And I agree that the indent widget would make more sense on the General tab, or another name, like Editor/Shell Preferences.

Another thought I had was Fonts should maybe be part of a Theme.  At the theme level (not at the tag level), define font name/font size and then have font bold at the tag level.  Spyder has that, so the function names (IDLE tag of `definition`) are bolded and the rest aren't.  It's subtle, but I find it pleasing to work with because function/class/method names stand out.  That would be after everything else though.

Another thought I had with the cycle in fonts:  A wdiget is clicked on, which calls the tkinter command callback.  But, the Tk variable is also updated which calls the trace function.  Those are the two paths.  What if the trace function called set_samples?  Then font_bold and font_size widgets wouldn't need the command argument.  I think `opt_menu_highlight_target` does that now because the command is commented out.

instead of:
click bold-toggle ~> set font_bold -> var_changed_font
       |
        \---> call set_sample

this:
click bold_toggle -> set font_bold -> var_changed_font -> set_sample