Where I live, I’d spend it on increasing parking availability at train stations, and/or run a lot more local buses that do a small (few kilometres) circuit around the station and ferry passengers to/from the station. Taking a bus to the station currently adds an unreasonable amount of time to the journey. It doesn’t matter how good trains are if I don’t live near a station and I can’t get there.

If we had to stick to transportation-specific improvements, I would use the money to eliminate bus fare for a year. (muni generates about $100M in fare, so really it would be enough money to eliminate fare for ~3 years.)

Unlike subway fare, bus fare doesn't prevent n'er-do-wells from getting on the bus (they just ignore the fare and get on anyway), and it probably increases ridership and gets some people out of their cars, which reduces congestion (public benefit and therefore deserving of government subsidy).