While looking around for something else I stumbled across this list on late night dining in Redwood City, Palo Alto/Menlo Park, Mountain View, Los Altos, Santa Clara, Milpitas,Cupertino, Sunnyvale,San Jose, Morgan Hill, Campbell, Los Gatos and Saratoga.
Don't be put off because it mentions Dennys. It also has places like Tacos Lupita in Morgan Hill which is open until 3 am and the Asian restaurants in Milpitas Square.
Don't know how current the list is but I know quite a few of those places are open.
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