A few ideas.
1)Offer to let employees purchase public transportation passes on a pre-tax basis. This might require partnering with the public trans office. I'm not sure. If you can go further, even providing a discount goes a long way. Here's an example of what is offered to employers in san diego:
http://www.sdmts.com/Marketing/EcoPass.asp
2)Services for cyclists, including bike racks/storage, showers, etc.
Just some quick thoughts, that's great your company is moving in that direction!