Consider using a car service. We used 101 Limo service, and they picked us from the airport and dropped us in Palo Alto. The fare was reasonable, the driver was reliable and courteous and knew the area well. Reservations are recommended.
When you are coming into Palo Alto, you have several choices of where to land. Each one of the airports are unique, Oakland (OAK), San Francisco (SFO) and San Jose (SJC) are all options when coming to Palo Alto based on where you are coming from. I always prefer a direct flight, which brings me into SJC often.
I might also consider copying this tip onto warnings and dangers... because there are a few things you have to worry about here.
The most important is the rental car situation. All of them share the same facility off the airport, and the same shuttle offers service to all terminals. If you are coming in on Southwest or American, you are in luck because those passengers get on first, so you may actually have room. All other airlines try to board full rental car shuttles.
Anyway, other than that this airport services Alaska Airlines, American, America West, Continental, Delta, Frontier, Jet Blue, Mexicana, Northwest, Southwest, and United.
I drove to Palo Alto but you can also take the Caltrain (public transportation). These directions take you to the downtown/Stanford Univ area. If you drive, take the Highway 101 to University Ave. Stay on this street when you exit & just keep driving (about 1 mile) until you reach boutiques lining the street on both sides. When you see all of this, you are in downtown!!
Either by Caltrain from SF and i guess they provide service from some other cities. Car is still one of the best way to get there i guess. There´s bus companies too going aroung the Bay area
If you don´t want to get to far but only around Palo Alto take a bike ride or go for skating. They also have a bussystem running on the campus area, and a bus service serving from SF and i guess some other cities aswell
Fly into San Jose or San Francisco Intl Airport. Taxis are your best bet from the airport. CalTrain is also a good way to get to Palo Alto from downtown San Francisco or San Jose.
Stanford runs free shuttles called the Marguerite around Stanford Campus and to downtown. Taxis aren't abundant on the street but you can call one and get service quickly. CalTrain runs along the Peninsula through Palo Alto with stops at University (Downtown)and California Ave. CalTrain is a good option for getting to San Francisco as it only costs about $4. Public buses are inexpensive but not especially convenient. Bikes are great for Stanford campus but not allowed on sidewalks downtown.
Taxi from SFO is inordinately expensive. They're likely to want full fare for the return trip as well as bringing you here.
I like Super-Shuttle myself. It costs somewhere around $28 for one, $34 for two, and drops you off at your destination. I don't recommend South Bay shuttle.
If you're really cheap, take the 50F bus. As an intermediate, take a taxi (if you must) to the Millbrae Caltrain station and take the train. It stops in downtown PA, and some trains also stop at California Ave.
PA is a reasonably bicycle-friendly town. Bryant is a bicycle boulevard running parallel to the bayshore. The main roads, as ever, are usable but not to be recommended.