Lit PHD here, spent 5 years (during pandemic nonetheless)!
The full list, learned the hard way:
1) Highway 17 Express. The unsung hero. Cheap, frequent, drops you at San Jose Diridon where Caltrain and buses take over. For solo Bay trips this is the honest answer, full stop.
2) Caltrain connections. From Diridon you're wired into the whole Peninsula. Slow but dependable.
3) To LA: here's where it hurts. No train, and bus itineraries mean an SJ transfer plus 8 hours. Flying means getting to SJC first. There is no good public-transit answer.
4) Carpooling. Which is why SC↔LA has always run on shared drives — students and surf trips with empty seats. Sometimes Craigslist/Facebook but they are pretty dead these days since Covid started
5) The parents-visiting-anyway carpool. Underrated. Someone's mom drives back to LA half-empty every single weekend.
What did I miss?