BayDad

Here’s a great summary list of kid-friendly train rides in the Bay Area and beyond:

Roaring Camp (In Felton): http://www.roaringcamp.com/
Tilden Park (Berkeley) http://www.ebparks.org/parks/tilden/
San Mateo Central Park: http://www.cityofsanmateo.org/index.asp?NID=718
Billy Jones RR in Los Gatos: http://www.bjwrr.org/
Niles Canyon Railway in Fremont: http://www.ncry.org/
Little Puffer in SF Zoo: http://www.sfzoo.org/openrosters/ViewOrgPageLink.asp?LinkKey=14106&orgkey=1900#littlepuffer
Train Town in Sonoma http://www.traintown.com/
Sacramento Rail Museum: http://www.csrmf.org/default.asp
Gilroy Gardens: http://gilroygardens.com

And of course, CalTrain, BART, and the VTA Light Rail.