The best values in the bay area are Monarch Bay San leandro and The Met in Oakland. I play them at least once a week.
Monarch is 7300+ yards from the tips, it'll really challenge you.
The Met is awesome too, great greens and a really great layout, no two holes look the same, and most holes can be played several ways (lay up or go for it, cut the corner with a draw or hang back, etc...) Course knowledge goes a long way here, that's why me and my buddies can play it over and over and not get tired of it. Sign of a good course I guess.
Both courses are around $35-45 green fees.
Yeah Lincoln is a total dump, don't go near it.
Harding is ok, but honestly not worth the $130 you'll pay as non resident.
The Reserve at Callipe is also a good choice, it's like two years new, located in Walnut Creek.
Also the Wente Course in Livermore is awesome, it hosts some Nationwide events. You're gonna need to book tee times well in advance.
Yeah in the bay area the best choices are actually in the east bay, the SF courses are really not up to par.
What other ones are you considering?