Please read the following SetupBuilder Code-Signing Guide:
Table of Contents
Part I Introduction
Part II FAQ
Part III Buying A Certificate - The Lindersoft "Deal"
Part IV Getting the Tools
Part V Setting Up SetupBuilder
Part VI Code-Signing Your Installer
Part VII Code-Signing Your Application Files
Note: CAPICOM.dll has been removed from the Microsoft Windows SDK for Windows 7 and .NET Framework 3.5 SP1.
Q3 2014 Updates:
As of late August 2013, all valid (not expired, not revoked) Comodo Code Signing Certificates can be used for Kernel-Mode Code Signing (Windows Vista and greater).
Microsoft has published a security advisory on "Deprecation of SHA-1 Hashing Algorithm for Microsoft Root Certificate Program". The new policy takes effect after January 1, 2016 and requires CAs to migrate to the stronger SHA-2 hashing algorithm.
In summary, Windows will cease accepting SHA-1 certificates on January 1, 2017. To continue to work with Microsoft platforms, all SHA-1 SSL certificates issued before or after this announcement must be replaced with a SHA-256 (SHA-2) equivalent by January 1, 2017. Organizations need to develop a migration plan for any SHA-1 end-entity SSL certificates that expire after January 1, 2017 and SHA-1 code signing certificates that expire after January 1, 2016. SHA1 code signing certificates that are time stamped before 1 January 2016 will be accepted until such time when Microsoft decides SHA1 is vulnerable to pre-image attack. Microsoft will give new consideration to the SHA deprecation deadlines in July 2015.
1. Customers should "renew" with SHA-2 end-entity and intermediate certificates.
2. Microsoft will cease trusting Code Signing Certificates using SHA-1 on January 1, 2016.
Most applications, servers and browsers now support SHA-2, however some older operating systems such as Windows XP prior to Service Pack 3, and some mobile devices do not.
For example: http://support.microsoft.com/kb/2763674
Before the SHA-1 algorithm is formally deprecated by Microsoft, it is important to ensure your organization and those relying on your infrastructure are benefiting from SHA-2 support by installing the latest version of the application or browser and applying all known security updates to your operating system.
Comodo will support only SHA-2 on all 3 year code signing certificates. They will also confirm policies at this time regarding 2 year SHA-1 code signing certificates.
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--Official COMODO Code Signing and SSL Certificate Partner