See [www.altamontpress.com]

And substitute liberally (or conservatively if you wear that color tie) referring to what Amtrak does.

Actually, there is a method in the fare madness. As Tom R says, ticket pricing is similar to airlines in that it varies by the minute (second?) and demand. There isn't much variation on the Cap Corridor BECAUSE it's non-reserved; there's no need for it to vary because there are no reservations. Though it does go up on and around holidays. The SJ *is* reserved so prices vary to fill seats at the highest fare feasible at the time you ask. A $10 fare to Emeryville from Stockton sounds like there are lots of empty seats on that segment so they'll practically give them away to get any revenue (reasonable; Stockton is a major bus transfer point on 4 of the SJ runs each way so there should be empty seats between there and the Bay Area).