From Wikipedia

Companies interested in participating in this certification should review the following criteria.

The application must install using an MSI or ClickOnce Installer. There are no exceptions to this requirement.
Applications must meet the basic certification criteria outlined in this document. Eligibilty Document

Have your engineers review the following two documents to identify if your application can meet the certification criteria.

Test Cases These are the tests your application must pass.

Waivers These test cases are eligible for waivers as specified in this document. No other test cases are eligible for waivers, do not assume they will be granted.

WHQL Testing

Windows Hardware Quality Labs testing or WHQL Testing is a testing process which involves running a series of tests on third-party (i.e. non-Microsoft) hardware or software, and then submitting the log files from these tests to Microsoft for review. The procedure may also include Microsoft running their own tests on a wide range of equipment, like different hardware and different Microsoft Windows editions.

For device drivers passing the WHQL tests, Microsoft creates a digitally signed certification file that, when included in the driver installation package, prevents Windows Vista from displaying a warning message that the driver has not been certified by Microsoft. Device drivers that have passed the WHQL tests are also made available for download using Windows Update.