Those are covered under other bond measures. LA has a multi-generation plan [1] for building out several new rail lines, busways, etc. It's harder to find an overarching document for the Bay Area because there are too damn many counties and transit agencies around here, but there are lots of projects -- BART to San Jose, Caltrain electrification, new rail lines and improved lines in SF, rebuilding the Dumbarton Rail Bridge -- that are in various stages of planning and construction.

[1] http://theplan.metro.net/