I replaced desktop bookmarks (screen-shot) thumbnails with logos and i added a little bit of transparency.

You can find png files in ~/.bookmarks/home-thumbnails and ~/.bookmarks/thumbnails.
Btw, i tried to change titles below logos i don't know where i can change them. It's not in ~/.bookmarks/MyBookmarks.xml and it's not in /usr/share/bookmark-manager/MyBookmarks.xml. Let me know if you find file in which are those titles.