In the \wwwroot\AdminScripts directory is the file adsutil.vbs, this is used to modify the Metabase from the command line.

adsutil SET w3svc/CheckCertMode 1 (To turn OFF checking)
adsutil SET w3svc/CheckCertMode 0 (To turn ON checking)

You can check the value with:

adsutil GET w3svc/CheckCertMode

Note that setting values prefixed with "w3svc/" sets the value globally - for all web sites running on the server. If there were a site with multiple web sites defined, then you can specify individual sites like:

adsutil SET w3svc/1/CheckCertMode 1  (For Site 1)
adsutil SET w3svc/2/CheckCertMode 1 (For Site 2)

You can list all defined values with:

adsutil ENUM w3svc/

There are optional values undefined by default (As is CheckCertMode) that can be found by reading documentation on the MetaBase.

In the upcoming IIS 6.0, the MetaBase is changed to a MetaBase.xml file which will be much easier to work with...