Berkeley is a university town, and the rhythm of the school year might affect your visit. It's easier to navigate the streets and find parking near the university between semesters, but there's also less buzz around town. Surprisingly, summer is chock-full of students attending the many summer sessions on campus. Moving-in weeks before the fall semester bring a massive influx of students and parents and other family members -- definitely not the best time to take a campus tour.
If you don't want to worry about finding a parking space, using public transportation to reach Berkeley or Oakland is ideal; BART has several central stops in both towns. For sheer romance, nothing beats the ferry; there's service from San Francisco to Alameda and Oakland in the East Bay.
BART trains can be packed during traditional morning and evening rush hours, but things are much less congested at other times. BART can get you from downtown San Francisco to a coffee shop in Rockridge in about 25 minutes. (It's closer to 30 minutes for farther points in Berkeley.)
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