I disagree with the above opinions.
Organizing your application and putting a table of contents to make it easier for the officer to locate things will show that you care about your application. Showing you're organized and took the time to present it well will have a positive affect subconsciously on your application to the person who opens the file. Yes, they will reorganize it, but at least the won't have to flip through hundreds of pages to find things they want to group together. A neat and tidy application that directs the person to exactly what they are looking for with ease is by far the best approach in my opinion.
We put sponsor forms, PA forms, and proof of relationship all in separate envelopes, each with its own table of contents that explained exactly what was included in a numbered format, as many of the items are actually not on the checklist especially the proof of relationship, and we wrote how many pages each separate thing consisted of. We then attached a sticky tab with a corresponding number as stated in the table of contents on a cover sheet for everything we submitted. Example on the table of contents "Tab 8- Proof of Upfront Medical Exam- 1 page" and then in the application a cover sheet that stated Proof of medical exam with a sticky tab with an 8 on it. We placed the table of contents directly underneath the barcodes and so anyone who opened our file could immediately find anything they were looking for.