I last did the Bay Tour in 2005, shortly after getting my private. Out of Oakland, you call ground and ask for "Bay Tour", which means you want to fly north over the Bay Bridge and hang a left into SF. Once they hand you off to approach, they ask you to advise intentions, and you want to go VFR under Bravo for a bit then the 101 transition. Fly over to the north side of the Golden Gate Bridge (direct or over Alcatraz; either way is very nice), turn southbound over the bridge then direct downtown SF. Once south of the bridge, advise that you want the 101 transition; most of the time they'll say "cleared into Bravo airspace, remain north and west of the Bayshore Freeway." That's the 101; if you're not familiar with the Bay Area, fly it first with an instructor. They'll hand you off to SF Tower. Approaching the hills to the east of SFO, they'll tell you to overfly SFO midfield; if they don't, ASK "do you still want us east of 101?" or you'll have a very large airplane taking off straight at you. Exiting Bravo they'll tell you "you are leaving bravo in 2 miles, contact San Carlos Tower." I think you can fly over their airspace and under Bravo, but why bother? DON'T turn over the Bay at this point, or your workload will spike and you might bust Bravo. Fly south to Palo Alto, being sure to request an airspace transition from Palo Alto Tower, before turning left over the Bay to return to Oakland. Contact Norcal approach for the approach into Oakland. The entire flight is probably 1 hour Hobbes (0.8 tach) in a 172.
When you're in Bravo, if there are ANY questions about what you want, ask them to suggest you a heading. If you mess up substantially, they'll point you at Japan ("Fly heading 270") until you're clear of Bravo, then they'll terminate you ("Radar services terminated, squawk VFR, frequency change approved"). Never had that happen to me, and I hope it remains that way
Flight schools: I used the Alameda Aero Club out of Oakland. Its Part 91, with the advantages and disadvantages inherent in that approach. Had I known, I would have waited and done a Part 141 when my job situation was more stable (I'm doing my instrument Part 141, and my flight instruction is free
thanks to work).