First, the standard disclaimer: IANAL but a random stranger.
I have been packaging an AGPL application(*) recently. It uses third party libraries distributed under jQuery, MIT, BSD (and some other) licenses. Here is how I have proceeded.
My main intents when I designed this were: be compliant and be fair. While the first one should be sufficient, the second one ensures that whoever tries to sue me for not getting it 100% right has to admit I have done things in good faith.
1) Source files: all my files have the AGPL header. All 3rd party files are left (mostly) unmodified, and therefore include their own license header.
2) LICENSE.txt, at the root of the package, contains the AGPL license text (as explained in the "How to Apply These Terms to Your New Programs" section).
3) A secondary license file, which I named LICENSE-3RD-PARTY.txt, also located at the root of the package, contains verbatim copies of ALL licenses. For each license, a header states which license it is, and which part it applies to. I also include the name of the copyright holders here - I reuse them somewhere else afterwards so it's worth the effort.
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The MIT License (MIT)
applies to:
- AJAX Upload, Copyright (c) Andrew Valums
- jQuery hashchange event, Copyright (c) 2010 "Cowboy" Ben Alman
- jquery.hotkeys, Copyright (c) 2010 John Resig
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Permission is hereby granted, free of charge [...]
4) README.txt, also at the root, explains that the software is AGPL (see LICENSE.txt) and uses third party libraries that are distributed under their own terms (see LICENSE-3RD-PARTY.txt)
5) In the on-line documentation, I have a License page that repeats the information from the readme: my software is AGPL, and it uses 3rd party components that are BSD/MIT/[...]. I have decided to keep this page cleaner and more readable, therefore only the name of the license is provided, with a link to the full text, and the name of the copyright holders with a link to their own website.
jQuery
Copyright 2013 jQuery Foundation and other contributors
http://jquery.com
MIT License
Data Driven Documents (D3)
Copyright (c) 2013, Michael Bostock <-- link to personal website, if any
http://d3js.org <-- link to software website
BSD-like license <-- link to license full text
[...]
6) Also in the on-line documentation, I have a Credits page, where I list the direct and indirect main contributors. I have for instance cited the PostgreSQL group, although PostgreSQL is not included in the download, but you need it to run the software. This would be a good place to place all acknowledgements that are either required or desired by the authors of 3rd party tools/libraries/etc.
7) Inside the software itself, the list of libraries along with the license and copyright holders, is repeated in the About dialog box.
To address your specific questions regarding inclusion of source code and file layout:
it is generally accepted to only link to the full source code of 3rd party packages. Consult each specific license to be sure, but IMHO providing the link should be enough. For instance, if you use a minified version of a library, you can provide the link to the standard download and be fine.
unless the 3rd party component explicitly demands that distributions keep the file layout identical, you can re-arrange things as you wish. Imagine you use web libraries, having each a css/ and a js/ directory, you can merge them together into a single lib/ directory, containing merged css/ and js/, or even scatter them all around your source tree - your choice.
And as a final note, I would more than welcome commenters who wave a hand saying "you are doing this wrong" and/or "you should also do that".
(*) This is not intended to be spam linking, but just to answer the "please provide examples" part of the question. Feel free, dear mods, to clear this link if this is against the rules.