Bay Area Airports
Three major airports serve the Bay Area; all are tolerably close to Palo Alto and Stanford, and all run long-distance flights. Take a look at airline schedules, and you may find better service to San Jose or Oakland than to San Francisco. (For instance, Southwest runs two direct one-stops between Baltimore and Oakland daily, but to get to San Francisco or San Jose one changes planes in Phoenix. All three airports run non-stops to Chicago, not to mention Portland and Seattle.) San Jose and Oakland are smaller, less intimidating airports, too.
San Francisco (SFO) is the big regional airport, with all the pluses and minuses of the breed. It tends to have more flights on major airlines (the cheapies, like Southwest, serve the other airports better), and fares on the majors tend to be slightly less expensive than to elsewhere. It's also huge, perpetually under construction, very easy to get lost in, and the only one likely to get socked in during the summer by fog. (Yes, fog. Remember that the coldest winter Mark Twain ever spent was a summer in San Francisco.) It's about 18 miles from Stanford, and traffic is not bad if you take the right roads (the I-380 to I-280 route is usually much better than US 101).
San Jose (SJC) is much smaller. Despite being the Silicon Valley airport, it is so low-tech that one of its two terminals still uses outside air-stairs for plane boarding. But it's small, unintimidating, and has baggage carousels that occasionally stun one with their efficiency. (This is the only airport where my bags sometimes arrive at the carousel before I do.) The area around the airport tends to get congested, and rush-hour traffic to Palo Alto is heavier than from SFO. But it's only 15 miles, and usually pretty managable. My usual airport of choice.
Oakland (OAK) is also small and easy to use, and the area around the airport is less congested than at SJC. But it's nearly 30 miles away, and freeway traffic (especially in the mornings going to Palo Alto, and the evenings going to Oakland) can be horrible. I only use it when it has the best flights and I'm not in a hurry to get to the airport. Ironically, Oakland has much better public transit to downtown San Francisco than SFO does, so that might be a factor if you're planning to spend time in the City, or Berkeley, in both of which a car is a bad idea (nor is one vital to get between Palo Alto and downtown San Francisco). [No longer true - Oakland's access to BART is now matched by SFO's - June 2004]
Shuttle bus service can be had from all three airports. I don't use them much myself, but the vans I see most on the roads belong to South and East Bay Airport Shuttle (1-800-548-4664, 408-225-4444), which serves all three airports. SuperShuttle (415-558-8500), the best-known service nationally, serves only SFO. [Also no longer true - it serves all three airports - Sept. 2007] You can catch these or other vans at the airport, and make reservations with them for your return. Generally speaking, hotels in this area don't run their own shuttle buses, but you can ask.
Trying to use public transit to Palo Alto from any airport is not a good idea.
Any adventurous souls planning to take Amtrak, or a bus, should book themselves to San Jose. Instructions for catching the commuter train to Palo Alto are here.
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