Traffic will fairly quickly stifle any of the romanticism and beauty surrounding a quick trip up to Mt. Tam or Tahoe. At some point during the 70mins in traffic it takes me to go the ~10 miles from SF to Mt. Tam I realize it just isn’t worth it.
I found commuting into SF to be a pain and heard that commuting from the east bay to SF or from SF to the south bay is also very tough. For awhile, I lived in Mill Valley (north of the GGB) and commuted in on the Ferry. I loved that experience on the days that it worked. But I also felt like I was way too tied to the ferry schedules.
If I could work from home (like I do now), I'd love to live in Sonoma again (fires aside). It's beautiful and a great place to ride your bike.
I'm in the Tri-Valley area, but we bought a while ago when prices were more reasonable. I'm used to long commutes, so they don't bother me so much. Pleasanton is the end of the Bart line, so you're pretty much guaranteed a seat if you use that to commute in. I work in the south bay, so for me it's car / bus on rainy days and motorcycle on the nicer ones. I can do a good chunk of work from home too, so that helps.
Livermore is a little too far out; the last couple miles of traffic are torturous. Oakland is pretty hit or miss. Berkeley is... uh... Berkeley. Fremont isn't a terrible choice, but there's always traffic no matter which direction you want to go. Anything near Milpitas smells like landfill. Walnut Creek and Lafayette are nice, but expensive.
I don't really know much about the peninsulas or Richmond.