Since the convention site's info is limited, here's some details based on experience:
transit.511.org (http://transit.511.org)
This is the Bay Area trip planner. Google Maps transit directions also works.
VTA Light Rail
Both of the main lines of the VTA Light Rail stops right in front of the convention center - stop is called Convention Center. It also stops in front of the Fairmont Hotel where badge pickup is. That stop is called Paseo de San Antonio.
(https://forums.fanime.com/proxy.php?request=http%3A%2F%2Fi66.photobucket.com%2Falbums%2Fh263%2Ffirstcultural%2FFanime%25202013%2520maps%2Ffanimecaliforniarailmapinset_zpsd55f9ff9.jpg&hash=affc2628ab182854763d28aa509405523f7cddc5)
Detail is from the California Rail Map, www.californiarailmap.com (http://www.californiarailmap.com)
Light rail runs from around 6am to midnight. Trains run every 15 minutes weekdays, 15-30 minutes on Saturday, and 30 minutes on Sunday and Memorial Day.
Schedules: http://vta.org/schedules/SC_901.html and http://vta.org/schedules/SC_903.html
VTA also has a lot of bus lines, their map is here: http://www.vta.org/schedules/schedules_bymap.html
VTA costs $2 a ride or $6 a day. Clipper Cards work on VTA.
VTA Bus 181 from Fremont BART
For folks coming from the East Bay this is likely to be the cheapest and fastest way.
The 181 stop at Fremont is on side of the station closer to the hills.
(https://forums.fanime.com/proxy.php?request=http%3A%2F%2Fi66.photobucket.com%2Falbums%2Fh263%2Ffirstcultural%2Ffremontbart_zps4b6b099f.jpg&hash=3343360875bed6f9445d25d8a3a20e2ded22bbfb)
Get off at 2nd and Santa Clara and walk 2 blocks to the Fairmont where registration takes place.
(https://forums.fanime.com/proxy.php?request=http%3A%2F%2Fi66.photobucket.com%2Falbums%2Fh263%2Ffirstcultural%2Fbus181_zpsf98f6435.jpg&hash=b7bed6bcd27c90386ae1b4cad9ac992b85ac2ab5)
San Jose Diridon Train Station
This station is served by Amtrak www.amtrak.com (http://www.amtrak.com), CalTrain from SF www.caltrain.com (http://www.caltrain.com), and the Altamont Corridor Express from Stockton www.acerail.com (http://www.acerail.com). Regional buses from Santa Cruz and Monterey also stop here. Megabus from LA also stops here.
VTA Light Rail stops at San Jose Diridon station, you just need to go down from the platform into the lower level walkway, walk under the tracks, and come up the opposite side. Light rail to the convention center is a 10-minute ride. There is also a weekday-only DASH shuttle that runs every 15 minutes and stops outside the station. http://www.vta.org/schedules/SC_201.html (http://www.vta.org/schedules/SC_201.html)
Amtrak schedules between Auburn, Sacramento, Davis, Oakland and San Jose: http://capitolcorridor.org/route_and_schedules/train_schedules.php If you are going in a large group buy a 10-ride ticket, they can be shared among many people and you get 10 rides for the price of 6. You can use half the rides going to the convention and the other half going home.
There are other Amtrak trains that stop in San Jose from various places in California and the west coast. The ride from Fresno is 4 hours and $31 each way. The ride from SoCal is 8-10 hours and $54-70 each way. There are no taxes or bag fees.
San Jose Greyhound Bus Station
This station is at 70 S Almaden Ave, San Jose, CA and is 2 blocks / 10 minute walk from the convention center.
Directions from the Airport
San Francisco: take BART to Millbrae, then Caltrain to San Jose.
Oakland: take BART to Fremont, then bus 181 to San Jose. There is an Amtrak train also but it doesn't run often enough to be a useful flight connection.
San Jose: take the free Airport Flyer shuttle bus to the VTA light rail station. http://www.vta.org/schedules/SC_10.html (http://www.vta.org/schedules/SC_10.html)
How long does the bus from BART take? I'm trying to time my trip out.
^ On average, about 40mins to the 2nd and Santa Clara stop. You can walk to the Fairmont from there.
http://www.vta.org/schedules/SC_181.html