I've done Mission/Monument peaks (Stanford Ave lot open until 9 or 10), Windy Hill (Alpine Rd parking until 9), Almaden Quicksillver and once with a Sierra Club group Orinda to Berkeley.
The best bet is to look for residential, on-street parking next to the trailheads or park entrances. I rarely see rangers in broad daylight so discrete after-dark hiking is unlikely to warrant attention.
Another option is to camp overnight and hike after dark. Angel Island and Mt Tam would be good spots In fact, now that I think about it, a full-moon hike on Mt Tam sounds fantastic; I may have to look into doing that one myself someday.