I guess it depends on what you call "peninsula". Mountain View is pretty far south and while the chamber of commerce would love to think they are part of the peninsula, well it screams out more South Bay/Silicon Valley to me.
But let's say that's the southern boundary and SF city limits are the north.
In that area, the public courses to consider are:
Shoreline GL - yes, great fun, some darn fine holes - conditions are never all that great though and methane gas fumes might put some off. John Krystynak - semi-regular here - is the expert, he plays there a lot. I used to when I lived nearby but haven't played it much in last 5 years.
Poplar Creek - former San Mateo muni, re-done by a group that included our very own Gib Papazian. Darn fun, quirky, vastly improved conditions, pretty darn good bang for the buck.
Palo Alto Muni - I see nothing really good there, but others do like it... It is a very fair test of golf... to me it's just kinda boring.
Crystal Springs - already discussed.
Sharp Park - oft-discussed in here, they call themselves MacKenzie but the course isn't in Wexler's Missing Links by accident. Could be so much, sadly isn't now.
That's it for 18-hole courses full-sized courses.
Add in the executive Emerald Hills - somewhat fun, very quirky, very cheap, but pasture golf conditions... and
Mariner's Point - 9 hole par 3 - very cool, linksy, night-lighted.. a recent fave of Chicago visitor shivas....
As you can see, it's slim pickings. It's not a stretch to say Shoreline is the best of the lot... though I might go for Poplar Creek as it is now.
TH
ps - I deliberately left out the HMB courses, as they are at a price range so greater than the others, the comparison is silly. Each of those would be clearly superior to the rest mentioned here... although maybe "clearly" isn't the proper word re the Old course there..... that's no great shakes.