Regarding point #2 in comment #70:

2. Some people had bad files on the local box (through proxy or direct
download) and for them the fix was "sudo mv /var/lib/apt/lists
/var/lib/apt/lists.old ; sudo mkdir -p /var/lib/apt/lists/partial"

The issue of apt creating bad files on disk in /var/lib/apt/lists/ has
been fixed in the quantal release of Ubuntu which will become Ubuntu
12.10.  Details regarding the fix appear in this changelog:

apt (0.9.7.5ubuntu2) quantal; urgency=low

  Merged from lp:~donkult/apt/experimental:

  [ David Kalnischkies ]
  * apt-pkg/contrib/strutl.cc:
    - support \n and \r\n line endings in ReadMessages

  [ Michael Vogt ]
  * lp:~mvo/apt/webserver-simulate-broken-with-fix346386:
    - merge fix for LP: #346386

I've tested that version of apt with the dummy-proxy provided by Colin
Watson and I received the following message in a terminal after running
apt-get update:

W: A error occurred during the signature verification. The repository is not 
updated and the previous index files will be used. GPG error:    
http://archive.ubuntu.com precise Release: The following signatures were 
invalid: NODATA 1 NODATA 2
W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/precise/Release
W: Some index files failed to download. They have been ignored, or old ones 
used instead.

After this I was able to use apt-get update again without having to
clear the files in /var/lib/apt/lists.  You may find some further
information about this bug in bug 346386.

We are currently working on getting this fix into the -proposed
repository for 12.04 and a comment will be added to bug 346386
indicating when it is available and how to test it.

I'll do some further research into update-manager's behavior if there
are bad files in /var/lib/apt/lists and open a new bug as needed.  There
are likely some user interface improvements that should be made if index
files are corrupt or fail to download.

** Changed in: apt (Ubuntu Quantal)
       Status: Triaged => Fix Released

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https://bugs.launchpad.net/bugs/24061

Title:
  GPG error with apt-get/aptitude/update-manager behind proxy (BADSIG
  40976EAF437D05B5)

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