There appears to be a hidden gotcha in the application for the Clean Air Vehicle sticker that allows HOV lane use. If you live in the SF bay area, you must also have a FasTrak account before you may apply for the sticker. The account costs $40 to activate.

And you must maintain a balance of at least $15 via a credit card.
However they may also be a hidden benefit. Carpoolers can use the FasTrak lanes at toll booths and in some places and are not charged the toll.
In my communte, I do not cross any bridges, nor travel on any toll roads, so I have no need for a FasTrak transponder. But in order to get the Clean Air Vehicle Sticker, you must have a FasTrak account. None of this has been mentioned in any of the news articles or forums, it is hidden in the fine print on the application for the sticker.
Will post more after I call the numbers..