I have a Windows 7 system that currently has a single update pending:
Windows Internet Explorer 9 for Windows 7 for x64-based Systems
If I try to install the update, Windows Update will:
Create a restore point
Fail with the error: Code 9C48 Windows Update encountered an error.
The event log for the event reads: 
  Installation Failure: Windows failed to install the following update with error 0x80070643: Windows Internet Explorer 9 for Windows 7 for x64-based Systems.
If you search the web for that error, there are many other people with the exact same issue.
Sadly, I am unable to apply the proposed solutions to my case, because I just installed this system.
There is nothing on it, except Windows 7. I installed the system and ran through the updates.
I also did the exact same process with this machine several times over the past few days due to a long-term test we just started.
I didn't have any problems with any Windows Update on the previous installation runs and I know I didn't do anything different this time because I followed the installation procedures instructions which are to be used during the test.
How did this happen and how do I solve it?
Further Investigation
So, as I always like to do, I ran the update again while running Process Monitor and dug up further details.
WindowsUpdate.log
First of all, there is a Windows Update log file located at C:\Windows\WindowsUpdate.log which I didn't know about. But I fail to see any significant entry in it, maybe you're more lucky:
2012-04-10  22:46:58:017     956    728 AU  AU received approval from Ux for 1 updates
2012-04-10  22:46:58:017     956    728 AU  AU setting pending client directive to 'Progress Ux'
2012-04-10  22:46:58:095     956    728 AU  BeginInteractiveInstall invoked for Download
2012-04-10  22:46:58:095     956    728 AU  Auto-approving update for download, updateId = {B33ACEC1-3265-4D01-9C37-AC0892E95ED9}.100, ForUx=1, IsOwnerUx=1, HasDeadline=0, IsMinor=0
2012-04-10  22:46:58:095     956    728 AU  Auto-approved 1 update(s) for download (for Ux)
2012-04-10  22:46:58:110     956    728 AU  UpdateDownloadProperties: 0 download(s) are still in progress.
2012-04-10  22:46:58:110     956    728 AU  #############
2012-04-10  22:46:58:110     956    728 AU  ## START ##  AU: Download updates
2012-04-10  22:46:58:110     956    728 AU  #########
2012-04-10  22:46:58:110     956    728 AU    # Approved updates = 1
2012-04-10  22:46:58:110     956    728 AU  AU initiated download, updateId = {B33ACEC1-3265-4D01-9C37-AC0892E95ED9}.100, callId = {35DF928B-B428-4BAC-8C63-55295967EFBB}
2012-04-10  22:46:58:110     956    728 AU  Setting AU scheduled install time to 2012-04-11 01:00:00
2012-04-10  22:46:58:110     956    728 AU  Successfully wrote event for AU health state:0
2012-04-10  22:46:58:110     956    728 AU  Currently showing Progress UX client - so not launching any other client
2012-04-10  22:46:58:110     956    bb8 DnldMgr *************
2012-04-10  22:46:58:110     956    bb8 DnldMgr ** START **  DnldMgr: Downloading updates [CallerId = AutomaticUpdatesWuApp]
2012-04-10  22:46:58:110     956    bb8 DnldMgr *********
2012-04-10  22:46:58:110     956    bb8 DnldMgr   * Call ID = {35DF928B-B428-4BAC-8C63-55295967EFBB}
2012-04-10  22:46:58:110     956    bb8 DnldMgr   * Priority = 3, Interactive = 1, Owner is system = 0, Explicit proxy = 0, Proxy session id = 1, ServiceId = {9482F4B4-E343-43B6-B170-9A65BC822C77}
2012-04-10  22:46:58:110     956    bb8 DnldMgr   * Updates to download = 1
2012-04-10  22:46:58:110     956    bb8 Agent     *   Title = Windows Internet Explorer 9 for Windows 7 for x64-based Systems
2012-04-10  22:46:58:110     956    bb8 Agent     *   UpdateId = {B33ACEC1-3265-4D01-9C37-AC0892E95ED9}.100
2012-04-10  22:46:58:110     956    bb8 Agent     *     Bundles 1 updates:
2012-04-10  22:46:58:110     956    bb8 Agent     *       {6D9A90B7-FAF9-4A47-9EFE-A506264873B3}.100
2012-04-10  22:46:58:110     956    bb8 DnldMgr ***********  DnldMgr: New download job [UpdateId = {6D9A90B7-FAF9-4A47-9EFE-A506264873B3}.100]  ***********
2012-04-10  22:46:58:110     956    728 AU  Successfully wrote event for AU health state:0
2012-04-10  22:46:58:110     956    728 AU    # Pending download calls = 1
2012-04-10  22:46:58:110     956    728 AU  ##  RESUMED  ## AU: Download update [UpdateId = {B33ACEC1-3265-4D01-9C37-AC0892E95ED9}, succeeded]
2012-04-10  22:46:58:313     956    bb8 Agent   **  END  **  Agent: Downloading updates [CallerId = AutomaticUpdatesWuApp]
2012-04-10  22:46:58:313     956    bb8 Agent   *************
2012-04-10  22:46:58:313     956    718 AU  #########
2012-04-10  22:46:58:313     956    718 AU  ##  END  ##  AU: Download updates
2012-04-10  22:46:58:313     956    718 AU  #############
2012-04-10  22:46:58:313     956    718 AU  Setting AU scheduled install time to 2012-04-11 01:00:00
2012-04-10  22:46:58:313     956    718 AU  Successfully wrote event for AU health state:0
2012-04-10  22:46:58:313     956    718 AU  Currently showing Progress UX client - so not launching any other client
2012-04-10  22:46:58:313     956    718 AU  Successfully wrote event for AU health state:0
2012-04-10  22:46:58:313     956    aac AU  Getting featured update notifications.  fIncludeDismissed = true
2012-04-10  22:46:58:313     956    aac AU  No featured updates available.
2012-04-10  22:47:00:107     956    aac AU  BeginInteractiveInstall invoked for Install
2012-04-10  22:47:00:107     956    aac AU  Auto-approving update for install, updateId = {B33ACEC1-3265-4D01-9C37-AC0892E95ED9}.100, ForUx=1, IsOwnerUx=1, HasDeadline=0, IsMinor=0
2012-04-10  22:47:00:107     956    aac AU  Auto-approved 1 update(s) for install (for Ux), installType=1
2012-04-10  22:47:00:107     956    aac AU  #############
2012-04-10  22:47:00:107     956    aac AU  ## START ##  AU: Install updates
2012-04-10  22:47:00:107     956    aac AU  #########
2012-04-10  22:47:00:107     956    aac AU    # Initiating manual install
2012-04-10  22:47:00:107     956    aac AU    # Approved updates = 1
2012-04-10  22:47:00:107     956    aac AU  ##  RESUMED  ## AU: Installing update [UpdateId = {B33ACEC1-3265-4D01-9C37-AC0892E95ED9}]
2012-04-10  22:47:13:773    2232    9fc Handler   : WARNING: Exit code = 0x8024200B
2012-04-10  22:47:13:773     956    718 AU    # WARNING: Install failed, error = 0x80070643 / 0x00009C48
2012-04-10  22:47:13:773    2232    9fc Handler :::::::::
2012-04-10  22:47:13:773    2232    9fc Handler ::  END  ::  Handler: Command Line Install
2012-04-10  22:47:13:773    2232    9fc Handler :::::::::::::
2012-04-10  22:47:13:851     956    a7c Agent   *********
2012-04-10  22:47:13:851     956    a7c Agent   **  END  **  Agent: Installing updates [CallerId = AutomaticUpdates]
2012-04-10  22:47:13:851     956    718 AU  Install call completed.
2012-04-10  22:47:13:851     956    a7c Agent   *************
2012-04-10  22:47:13:851     956    718 AU    # WARNING: Install call completed, reboot required = No, error = 0x00000000
2012-04-10  22:47:13:851     956    718 AU  #########
2012-04-10  22:47:13:851     956    718 AU  ##  END  ##  AU: Installing updates [CallId = {FCFF2A5C-25AB-4FB9-AB2B-35C65CCA6A9F}]
2012-04-10  22:47:13:851     956    718 AU  #############
2012-04-10  22:47:13:851     956    718 AU  Install complete for all calls, reboot NOT needed
2012-04-10  22:47:13:851     956    718 AU  Setting AU scheduled install time to 2012-04-11 01:00:00
2012-04-10  22:47:13:851     956    718 AU  Successfully wrote event for AU health state:0
2012-04-10  22:47:13:851     956    498 AU  Getting featured update notifications.  fIncludeDismissed = true
2012-04-10  22:47:13:851     956    498 AU  No featured updates available.
2012-04-10  22:47:14:366     956    168 AU  No featured updates notifications to show
2012-04-10  22:47:14:366     956    168 AU  UpdateDownloadProperties: 0 download(s) are still in progress.
2012-04-10  22:47:14:366     956    168 AU  Triggering Offline detection (non-interactive)
2012-04-10  22:47:14:366     956    168 AU  AU setting pending client directive to 'Install Complete Ux'
2012-04-10  22:47:14:366     956    168 AU  Changing existing AU client directive from 'Progress Ux' to 'Install Complete Ux', session id = 0x1
2012-04-10  22:47:14:366     956    168 AU  Successfully wrote event for AU health state:0
2012-04-10  22:47:14:366     956    b78 AU  #############
2012-04-10  22:47:14:366     956    b78 AU  ## START ##  AU: Search for updates
2012-04-10  22:47:14:366     956    b78 AU  #########
2012-04-10  22:47:14:366     956    b78 AU  ##  RESUMED  ## AU: Search for updates [CallId = {0198DD3A-D7B0-48F5-A77D-795F8A1BDCE8}]
2012-04-10  22:47:16:097     956    718 AU    # 1 updates detected
2012-04-10  22:47:16:097     956    718 AU  #########
2012-04-10  22:47:16:097     956    718 AU  ##  END  ##  AU: Search for updates [CallId = {0198DD3A-D7B0-48F5-A77D-795F8A1BDCE8}]
2012-04-10  22:47:16:097     956    718 AU  #############
2012-04-10  22:47:16:097     956    718 AU  No featured updates notifications to show
2012-04-10  22:47:16:097     956    718 AU  Setting AU scheduled install time to 2012-04-11 01:00:00
2012-04-10  22:47:16:097     956    718 AU  Successfully wrote event for AU health state:0
2012-04-10  22:47:16:097     956    718 AU  Successfully wrote event for AU health state:0
2012-04-10  22:47:16:113     956    55c AU  Getting featured update notifications.  fIncludeDismissed = true
2012-04-10  22:47:16:113     956    55c AU  No featured updates available.
2012-04-10  22:47:18:780     956    bb8 Report  REPORT EVENT: {27479C66-E930-4F9C-AFF2-27EDD76DED8F}    2012-04-10 22:47:13:773+0200    1   182 101 {B33ACEC1-3265-4D01-9C37-AC0892E95ED9}  100 80070643    AutomaticUpdates    Failure Content Install Installation Failure: Windows failed to install the following update with error 0x80070643: Windows Internet Explorer 9 for Windows 7 for x64-based Systems.
2012-04-10  22:47:18:780     956    bb8 Report  CWERReporter::HandleEvents - WER report upload completed with status 0x8
2012-04-10  22:47:18:780     956    bb8 Report  WER Report sent: 7.5.7601.17514 0x80070643 B33ACEC1-3265-4D01-9C37-AC0892E95ED9 Install 101 Unmanaged
2012-04-10  22:47:18:780     956    bb8 Report  CWERReporter finishing event handling. (00000000)
WU-IE9-Windows7-x64.exe
The actual update that is executed is downloaded and stored at the following location:
C:\Windows\SoftwareDistribution\Download\Install\WU-IE9-Windows7-x64.exe
Executing that file manually, results in the following error message:
IE9_main.log
The IE9 installer/updater also creates an own log file located at
C:\Windows\IE9_main.log
For the update session in question, the installer logged:
00:00.000: ====================================================================
00:00.016: Started: 2012/04/10 (Y/M/D) 23:10:53.897 (local)
00:00.032: Time Format in this log: MM:ss.mmm (minutes:seconds.milliseconds)
00:00.063: Command line: "C:\Windows\SoftwareDistribution\Download\Install\WU-IE9-Windows7-x64.exe" 
00:00.078: INFO:    Setup installer for Internet Explorer: 9.0.8112.16421
00:00.094: INFO:    Previous version of Internet Explorer: 9.0.8112.16443
00:00.110: INFO:    Checking if iexplore.exe's current version is between 9.0.6001.0...
00:00.125: INFO:    ...and 9.1.0.0...
00:00.141: INFO:    Maximum version on which to run IEAK branding is: 9.1.0.0...
00:00.156: ERROR:   A newer version of Internet Explorer is already installed on the system.
00:00.188: ERROR:   Internet Explorer version check failed.
01:03.789: INFO:    Setup exit code: 0x00009C48 (40008) - A more recent version of Internet Explorer is installed.
01:03.820: INFO:    Scheduling upload to IE SQM server: http://sqm.microsoft.com/sqm/ie/sqmserver.dll
01:03.852: INFO:    SQM Upload returned 403
01:03.867: INFO:    Cleaning up temporary files in: C:\Windows\TEMP\IE978E.tmp
01:03.883: INFO:    Unable to remove directory C:\Windows\TEMP\IE978E.tmp, marking for deletion on reboot.
01:03.898: INFO:    Released Internet Explorer Installer Mutex
Which pretty much confirms what the error message says when executing the update manually; it's simply already installed or even obsolete because a newer version is installed.
So, why does it try to keep installing the update?
Possible solutions?
Uninstalling Windows Internet Explorer 9 and manually installing the cached C:\Windows\SoftwareDistribution\Download\Install\WU-IE9-Windows7-x64.exe will result in the same error after applying all pending updates.
Applying the FixIt for the issue You receive “0x80070643” or “0x643” error codes when you try to install .NET Framework updates through Windows Update or Microsoft Updates will not resolve the issue.
Applying the suggested solution for the issue Error message when you try to install updates by using the Windows Update or Microsoft Update Web site: "0x80070003" will not resolve the issue.
Running the FixIt Automatically diagnose and fix common problems with Windows Update does report having resolved issues with Windows Update, but didn't resolve the issue.
Running the FixIt for the issue How to troubleshoot Windows Update or Microsoft Update when you are repeatedly offered an update does not resolve the issue. Neither with normal nor with aggressive settings.