Bookmarks are a way for you to save images when you are reading and revisit them later. When you bookmark a file, the image is saved in your bookmarks/ directory (which can be configured to be stored in a location other than config/). These bookmarks can be viewed from the UI either through Series Detail page and using Context options or from User Settings and clicking Bookmarks tab.
From the user settings tab, you can see all your bookmarks. You can download all images in a zip or delete all files. Likewise, you can view each and every image by clicking the series title or using the eye button to go the series itself.
From here, you have the same options but can remove individual images that might have been saved that you don't want any longer.