I am certainly anal about organization but i let that go for this. I followed the order of the list of supporting documents on the UK visa site and sectioned out the sections. I put the sections in paper clips and then had those little post-it note flags and labled it that way. I had thought about an expanding folder or in separate folders, but that just adds weight and cost. Some people do a table of contents type thing as well. I JUST got all my stuff back (including my passport with my shiny new spouse visa...eep!! still so excited!) and it there was no paper clips to be seen and one or two little post it flags left...so literally don't driver yourself nuts 
good luck!!
Congratulations!!!
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So it was all messy?
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Boo. Did you staple stuff together (if so was unstapled?)
I was thinking post-it flags too, one color per section. So for example, all maintenance items will be green (wage slips, bank statements, other income, etc.) and accomodation will be blue (land reg docs, letter of invite, council tax bill). Makes sense right? And then I was going to staple each sub section (land reg docs, all 4 pages stapled). I don't love paper clips bc they come off too easy for my liking.
Please do tell more!
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What sections did you have if you don't mind my asking? I was thinking these section headers:
IndexApplicant Statement (brief letter, explain some stuff more that there was no room for on app, our intent) then my passport and photo
Sponsor Statement (brief letter of support of my app, mirroring mine a bit) passport copy and birth cert.
Co-sponsor Statement (letter of invite to stay, offer of financial help should we need it just in case) passport copy
Accommodation (Land Reg Docs, Council Tax Bill, Photos, etc.)
Maintenance (2 main sections: a) our savings and financial details, b) co-sponsor's documents, of which there is a ton bc father in-law owns his own business and his income is, shall we say, diverse)
Relationship (Marriage Cert., photos)
As of yet Unnamed Section (traffic offenses and other miscellanea, hard to explain so no name yet until finalized)
Each Section will have a brief explanation of things contained. The reason I want to do this is because there's way too much to explain in a letter (4 pages seemed excessive!) Also, if something did get lost I hope and index plus section header sheet listing/explaining what's contained might draw their attention to it.
Any opinions?