If you flew into SFO for Clojure/west, let me be the first to apologise. You have a long journey ahead of you.
Alex posted some links to the airport shuttle in the Guidebook app. Since I work in San Francisco occasionally but attend class in Downtown San José, I'm all too familiar with the arduous task of getting from one to the other. Here's how I do it.
I don't know anything at all about non-public transit options and I don't drive so please don't ask me what to do with your car, I genuinely don't know.
If you run into trouble with my instructions I will do my best to get you out of it again. You can reach me on Twitter as @nuclearsandwich or text me 408.256.0278. I don't generally answer phone calls.
See you at the conference!
Unfortunately, you're probably arriving before 7PM today. Which means that in order to get to Millbrae station, which you'll need to do to catch Caltrain, you'll need to board a Pitsburg/Bay Point train (Yellow on the BART map) and go back ONE STOP to San Bruno. Get off there but don't leave the platform or you will have to pay extra, just wait a few minutes for a Millbrae train. If you're arriving after 7PM tonight, The Millbrae line stops at SFO and you can get on a Millbrae bound train directly from the airport. The fare from SFO to Millbrae via BART is $4 as long as you don't exit the platform at San Bruno.
I'm slightly biased, I love riding Caltrain and have since I was a kid. However, arriving in the middle of the day is haphazard since the schedule is a bit funny.
When you get to Millbrae, go upstairs and through the BART faregates. Turn left and you'll see two large red vending machines and stairs leading down to the Southbound Caltrain platform. Stop at the vending machine and purchase a one-way ticket to Zone 4. It'll be about $8. Depending on how lucky you are, the next train could be very soon or an hour away. I've scraped the relevant trains out of the Weekday Caltrain Timetable and built a table for you. Please remember to purchase a ticket as you cannot buy them on the train and the citation is $300. Trust me, I forgot to renew my monthly pass once.
Millbrae | San José
Departure | Arrival
11:31 | 12:38
12:31 | 13:38
13:31 | 14:38
14:31 | 15:38
15:31 | 16:39
15:55 | 17:00
*16:25 | 17:06
16:56 | 17:55
*16:49 | 17:32
17:14 | 18:16
*17:30 | 18:11
17:56 | 18:56
*17:49 | 18:32
18:14 | 19:16
*18:30 | 19:11
18:56 | 19:55
*18:49 | 19:32
19:14 | 20:12
19:54 | 21:01
21:04 | 22:11
22:04 | 23:11
23:04 | 00:11
00:25 | 01:32
* Faster, but more crowded express commuter train.
There's a free shuttle that runs between Diridon Station and Downtown that runs quite frequently. When you arrive at San Jose (make sure you get off! Some of the trains continue on). When you exit the platform, go straight directly up the ramp (you'll know it) and out the door. You'll see a large lot where all the buses park. Head right to the island nearest to the parking lot. You should see a sign for DASH and one or two other buses. I don't advise you get on any of the large white buses. The one you'll be getting on is a smaller red bus.
Once you're on, you have two choices. You can get off at First and San Fernando and walk down first street to the Marriott map or take the bus completely around past San Jose State and get off at San Carlos and Market or San José Convention Center, directly across the street from the Marriott.
If your bags are large or heavy, I recommend taking the bus the whole way. If you want a pleasant walk down 1st Street and you've got only a small bag feel free to get off early.
Important: The shuttle's last trip is at 7PM. If you're arriving later than that I'll edit this gist to include the best regular VTA bus to take for this leg but right now I need to get back to my homework.