A bookmark is way to define areas of your workspace for easy access. The bookmark shades an area, usually one that is carrying out a specific task, so you can easily move to it in the workspace.
Bookmarks play an important part in FME for a number of reasons:
places a marker for quick access to a certain area
divides a workspace into different, clearly marked sections
organizes a workspace so you can move sections of transformers at one time
See Using Bookmarks in a Workspace.
Other than using bookmarks for general organization and ease-of-use, here are some additional reasons:
Remembering why you created a workspace: Bookmarks can help remind you why you created a workspace, and how it works.
Deciphering someone else's workspace: Bookmarks can clarify the purpose of a workpace, and provide the necessary context for determining how it works.