Depends on where exactly you'll be working...
...but if it's downtown Berk and downtown Oak, I'd look at the Elmwood (South Berkeley) and Rockridge (North Oakland) neighborhoods. Both are relatively safe, have a lot to do, and have a number of housing options that feel less urban (e.g., houses for rent, 1920s-era fourplexes, small yards, etc.). That said, both are also pricey!
Rockridge is great because it's got a BART station (to downtown Oak and then into SF), but unfortunately that line doesn't run into Berkeley, so you'd be stuck with the bus for the daily commute. The 1-Rapid (a new limited-stop line that runs down Telegraph Avenue from the Berkeley campus to downtown Oakland and beyond) is a nice commute. Avoid a place where you'll have to rely on the 51 (which runs down College Avenue and is pretty unreliable--we actually live right on the 51, but I walk the four blocks to the 1-R because it cuts 15-30 minutes off my commute, on average!)
If one or the other of your commutes is *not* to the downtown area, I'd look closely at what the transit options are for that commute and plan accordingly. Check AC Transit (bus service, pretty decent for most lines) and BART ("subway," but often 15-minute headways between trains so you have to plan ahead) websites for info on this. Also be cognizant of where the freeways are, as you will hear/feel both BART and the freeway if you live too close to either.
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