bgbc has a problem—in the East Bay, the OP has had no luck finding cafés with the right vibe for working in the middle of the day. San Francisco favorites include Farley's and Epicenter, which win points for a diverse, friendly crowd of worker bees and artist types, not-too-loud music, and decent-to-great coffee. Also, everybody must check their attitude at the door; bgbc isn't looking for "sneering hipsters, sneering baristas, rows and rows of sullen wifi-warriors."
Top recommendations for Oakland and Berkeley include Local 123, which bgbc reports is not too crowded in the afternoon and mostly has a graduate student crowd; they serve Flying Goat Coffee from Healdsburg, and a past thread recommended the espresso drinks there, particularly the soy latte.
Another new favorite is Remedy Coffee, which does brisk business in walk-through ordering but isn't too crowded in the morning for those who want to hang around for a while. Earlier this year, abstractpoet praised Remedy's outstanding cappuccino (made with Ritual beans) and scones.
Local 123 [East Bay]
2049 San Pablo Avenue, Berkeley
Remedy Coffee [East Bay]
4316 Telegraph Avenue, Oakland