Inform participants of environmentally responsible transportation options. Use your communications (such as the registration confirmation email) to tell them the best way to get from their airport to the hotel to the convention center.
If walking is the best way to get around, give them pedometers (sponsorship opportunity) and have a contest for the most miles walked. Make it fun!
If shuttles cannot be avoided, minimize the shuttle times and area covered to save time and the environment e.g. don't shuttle for distances less than 6 blocks, but do have transportation available for those with special needs.
When using a transportation company, request their environmental policies as part of the RFP process. Require the use of alternative fuels (bio-diesel, electric, ethanol, natural gas) or hybrid vehicles and avoid unnecessary idling. Put it in the contract!