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It should be simple to have an option for a Background colour for Bookmarks say in a number of limited colours. This will emulate the colored stick on tabs many lawyers use to denote particular topic within bundle - eg. every reference to C100 product. Sometimes you do not need text - just colour
This should be compbined with the option just to display the coloured bookmarks in the bookmarks pane.
This should be very simple to implement and can remain optional for those who dont want to use it.
You also need a bookmark editor to reorganise book marks. Drag and drop only works so far but moving a bookmark from bottom of a long list to the top is a pain.
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I am not aware of any bookmark editor. You should be able to right mouse click on a bookmark and set the color property or use JavaScript to change the color of a bookmark. As for moving, you could move it in stages.
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It's not simple at all, actually. The way the bookmarks appear is defined by a part of the PDF Specifications ISO (section 12.3.3 Document Outline, to be precise), and changing it is a long and complicated process. You can't just decide to add an option to have background colors to a bookmark and implement it in your own "PDF Bookmarks Editor" app, because it's not going to work anywhere else.
However, with a bit of creativity you can achieve something similar, which will stand out in the bookmarks panel.
For example, I've used the FULL BLOCK Unicode character (█) multiple times and set the bookmark color to pink to achieve this:
You can experiment with different characters and maybe get better results...
I do agree that Acrobat could do a better job of allowing you to move bookmarks around, though.
However, this can be done using a custom-made script.