If you arrive in Juneau by plane or by ferry without your car you may want to either rent a car or travel by taxi.  The following is a listing of rental car and taxi companies in the Juneau area:

Budget Rent-a-Car:  Their Juneau office has a key drop-off box at the Marine Highway Ferry Terminal for easy car return for ferry passengers.

Evergreen Taxi:  Reserve a taxi for a tour, to meet you at the airport or ferry, or to get around town.  For immediate dispatch, phone (907) 586-2121.

Rent a Wreck: They are extremely accomodating. They have a cruise ship location, and a second location. Will make arrangements for ferry terminal pick up, and will drive you to the airport after dropping car off.   (888) 843-4111

Note: Rent-a-Wreck apparently is now called Juneau Car Rental Company. http://www.juneaucarrentals.com/ .  They were super friendly and cheaper than other options. Definitely would recommend them for cruise ship passengers, since they're within walking distance of most of the docks.