Chris Stauffer at myITForum.com

How to Find IE6 or older in your Environment with SMS or SCCM

Note: This only works for IE6 Sp1 or older. Any newer versions can be found in the Registry and in Add/Remove Programs.

According to MS the correct way to find the version of IE6 is to collect the SHDOCVW.dll 
Use "Software inventory Client agent" Check the Inventory Collection tab and add the  SHDOCVW.dll   Specify the location of %windir%\system32\
Then create a collection like this:

Machines with IE6 Sp1

select SMS_R_System.ResourceID,SMS_R_System.ResourceType,SMS_R_System.Name,SMS_R_System.SMSUniqueIdentifier,SMS_R_System.ResourceDomainORWorkgroup,SMS_R_System.Client from SMS_R_System inner join SMS_G_System_SoftwareFile on SMS_G_System_SoftwareFile.ResourceID = SMS_R_System.ResourceId where SMS_G_System_SoftwareFile.FileName = "SHDOCVW.dll" and SMS_G_System_SoftwareFile.FileVersion >= "6.00.2800.1106" and (SMS_G_System_SoftwareFile.FilePath = "c:\\windows\\system32\\" or SMS_G_System_SoftwareFile.FilePath = "c:\\winnt\\system32\\")

Need IE6 SP1

select SMS_R_System.ResourceID,SMS_R_System.ResourceType,SMS_R_System.Name,SMS_R_System.SMSUniqueIdentifier,SMS_R_System.ResourceDomainORWorkgroup,SMS_R_System.Client from SMS_R_System inner join SMS_G_System_SoftwareFile on SMS_G_System_SoftwareFile.ResourceID = SMS_R_System.ResourceId where SMS_G_System_SoftwareFile.FileName = "SHDOCVW.dll" and SMS_G_System_SoftwareFile.FileVersion < "6.00.2800.1106" and (SMS_G_System_SoftwareFile.FilePath = "c:\\windows\\system32\\" or SMS_G_System_SoftwareFile.FilePath = "c:\\winnt\\system32\\")

And reports like this one

SELECT DISTINCT
                      v_FullCollectionMembership.SiteCode, v_GS_SYSTEM.Name0 AS [Machine Name], v_GS_SoftwareFile.FileVersion AS [IE Version],
                      v_R_System.Operating_System_Name_and0, v_GS_SoftwareFile.FilePath
FROM         v_GS_SoftwareFile INNER JOIN
                      v_GS_SYSTEM ON v_GS_SoftwareFile.ResourceID = v_GS_SYSTEM.ResourceID INNER JOIN
                      v_R_System ON v_GS_SYSTEM.ResourceID = v_R_System.ResourceID INNER JOIN
                      v_FullCollectionMembership ON v_GS_SYSTEM.ResourceID = v_FullCollectionMembership.ResourceID
WHERE     (v_GS_SoftwareFile.FileName = 'shdocvw.dll') AND (v_GS_SoftwareFile.FilePath = 'c:\windows\system32\' OR
                      v_GS_SoftwareFile.FilePath = 'c:\winnt\system32\') AND (v_GS_SoftwareFile.FileVersion > '6.00.2800.1106' OR
                      v_GS_SoftwareFile.FileVersion = '6.00.2800.1106') AND (v_FullCollectionMembership.CollectionID = 'sms00001' )
ORDER BY v_GS_SYSTEM.Name0

MS has this KB article. It use to have one that checked the version of the SHDOCVW.dll
I can not find the KB for that anymore. All i can find is this:
http://support.microsoft.com/kb/164539

Edited:

Here is the KB article that explains the DLL Versions.

http://support.microsoft.com/kb/969393

Determine the version of Internet Explorer by using the Shdocvw.dll file:

For Internet Explorer 3.0 through 6.0, the browser is implemented in the Shdocvw.dll (Shell Document Object and Control Library) file. You can use the version of the Shdocvw.dll file to determine the version of Internet Explorer 3.0 through 6.0 that is installed on your computer. To determine the version of Internet Explorer 7, you must use the version of Iexplore.exe. To do so, follow these steps:

1. Click Start, point to Find, and then click Files Or Folders.
2. In the Named box, type shdocvw.dll, and then click Find Now.
3. In the list of files, right-click the Shdocvw.dll file, and then click Properties.
4. Click the Version tab.
5. Repeat steps 2 through 4, but in step 2 type iexplore.exe. If the version of Iexplore.exe is 7.x, then Internet Explorer 7 is installed. Use the table of Internet Explorer versions earlier in this article to compare the version number to released versions of Internet Explorer 7.

This table lists the different versions of the Shdocvw.dll file and the corresponding versions of Internet Explorer.