When I applied last summer, this is how I presented my stack... nothing fancy schmancy other than the use of some colour paper (for my own benefit/sanity) to separate the different sections of information. I didn't list any of the items I sent because I figured that they're smart enough to know what they're looking at and I went through the stack myself countless times just to make sure every "i" was dotted and every "t" was crossed:
Biometric Appointment Paperwork
Application form with appendix (because I had more passport and trip information than space allowed)
Pink sheet of paper to separate, with my name (last, first), Date of Birth, Canadian Citizen, Visa Reference Number written on the upper left hand corner
Applicant Letter
Passport
Birth Certificate
Travel Itinerary for my flight from Vancouver to London dated October 1, 2012
Green sheet of paper to separate, with Ed's name (last, first), Date of Birth, British Citizen written in the upper left hand corner
Ed's Sponsor Letter (Ed being my then fiance, now husband)
Copy of Passport Bio Page
Original Long Form Birth Certificate
P60
Banking Info
Mortgage statement
Yellow sheet of paper to separate, with the words "Supporting Documentation" written in the upper left hand corner
Air travel itineraries for trips to meet in Vancouver & London
Receipt for Engagement Ring
Skype conversation history screen shots
Selection (about 10 double sided pages) of emails dating from first email to just after first IRL meeting
8 "Photo shop" photos (i.e. the type that one used to get from those "One Hour Photo" type places) of Ed and myself and our families
A selection of digital photos downloaded from emails and printed on A4 paper
Brochure from the Church of England Church we were married at
Copy of Wedding Breakfast contract
I took the time to print everything out on A4 paper. If you can't find A4 size paper at your local Office Depot/Staples, ask them if they are able to cut 8.5" x 14" (Legal size) paper down to size for you... they should be able to do this as A4 is a standard size that is slightly taller and slightly narrower than 8.5" x 11" paper and even the old school paper cutter we had at work had the markings to cut paper to size)
I also included copies of all the important stuff (banking information, P60, Mortgage statement, etc) that I wanted them to return. On all of the copies, I stamped as "Copy" and in addition to that and on the copies and non-important primary documents (Skype Screen shots, itineraries, envelope holding my birth certificate etc) I wrote my Visa Application Reference Number (VARN) in the upper right hand corner, just in case a sheet of paper went astray the ECO could see the VARN and would know which application it belonged to. Yes, I know it was a little OCD of me to do all of that, but my whole future happiness rested in that stack of paper I sent and I just didn't want anything to go wrong.
Good luck to you!