Johnathan,
Here is my two cents on the courses that are worth getting to, either I have played them or had them strongly recommended...I've never heard Dr. MacKenzie was ever at Harding park. I want to say Willie Watson, and Jack Fleming.
Public Courses
San Geronimo Golf Club Yes (vernon macan)
Harding Park Golf Course* Yes (watson, fleming, PGA tour)
Lincoln Park Golf Club No hurry
Pasatiempo Golf Club* Yes
Indian Valley Golf Club
Embarassed to say have not heard of it
Dark Horse Golf Club Yes (Keith Foster)
Pacific Grove Municipal Golf Links Yes
Haggin Oaks Golf Course* No hurry, with Time Machine yes
Northwood Golf Club* Yes
Sharp Park Golf Course* Yes, gnarliest cypress trees I have seen
DeLaveaga Golf Course No hurry
Add ons:
Saddle Creek Yes
Roddy Ranch Fast and Firm, windy, Yes
Stevinson Ranch Heard it is cool.
Wente Vineyards No Hurry, concert series Yes
Metropolitan Better than I expected, but no hurry
Gleneagles 9 Yes, I've heard it is very fun
Pajaro Valley low price range, nice atmosphere
Seascape priced to high, but fun and nice atmosphere
Private Courses
Mayacama Golf Club Yes
San Francisco Golf Club Yes
The Olympic Club Yes
Cypress Point Club* Yes
The Meadow Club* Yes
Marin Country Club No Hurry
Monterey Peninsula Country Club Yes
Fountain Grove Golf and Athletic Club No Hurry
Napa Valley Country Club No Hurry
Claremont Country Club* Yes
Green Hills Country Club* Heard it is fun, never been
Lake Merced Golf Club* No Hurry, in Time Machine Yes
Morgan Creek Yes, unique and good (Kyle Phillips)
Preserve in Carmel Cool setting, underachieves though, Yes
Penninsula (beresford) Yes (Ross, Ron Forse resto, reno)
Add ons:
Orinda Country Club (willie watson, strong fairway contours, few fairway bunkers, small greens)
Los Altos G & CC (jeff brehaut, and julie inkster play it as home course)
I live in the area, so let me know if you are heading out this way.