Since San Jose went from the gateway to Silicon Valley to the Heart of Silicon Valley, I feel like San Francisco, which is actually part of the Peninsula, can be part of SV.
South Bay -- Platforms, infrastructure, embedded systems, established technologies, emphasis on availability and reliability. This is what the San Francisco startups rely on to make sure their new web startup doesn't fall over at the first sign of traffic.
One might see this as the traditional Silicon Valley maturing and even stagnating in comparison to San Francisco's young, hip, fast-moving culture, but I don't think it's reasonable to treat them as a unified entity.
That said the Bay Area definitely has an OSI model going, with the lowest levels in the SE extreme (santa clara, san jose), higher levels NW (Mt View, Palo Alto), and software applications all the way to SF.