Hey there - i actually just moved from NYC to the Bay area one month ago, you can find my blog about the drive cross country on my profile. That being said, here is what I can offer you:
1) I came from NYC and was not hungry for hills, and did not mind a commute as I was used to the train.
2) I went all over 15 neighbohoods in San Francisco and, for the price range, up to $1,500 I was not satisfied
- this is a low price range by the way, not that realistic for a great place within the city
3) I spent one day in Oakland - Jack London Square, and fell in love with the whole thing.
Since then I have explored alot more, I would totally live in Berkeley, the whole East Bay, even Alameda. You get alot of bang for your buck, but you are missing out on the city scene. The commute in the morning is awesome if you carpool (maybe 20 minutes over the bridge). My office is in the mission, so right over the Bay Bridge and you are here.
BART sucks IMHO, it doesn't run past midnight and the pricing is ridiculous - so unless you are REALLY going to ride the BART or MUNI, who cares about paying a toll?
Parking is AWESOME in the East Bay. My apartment in Jack London Square is $1,350, is 3-5 years old, includes a washer/dryer, dishwasher, microwave, gym and parking. The marina has restaurants, cool bars and a farmers market, Whole Foods, Trader Joes and more are nearby. BART is there if you want it too and the highways are easily accessible.
Anyway, pick a price range and get out there. I found that there were some good deals. I found a great 1 BR with balcony, in the Sunset neighborhood of SF, for $1300 with parking. The neighborhood I am talking about in the east Bay, Jack London Square is ZIP code 94607, below are some buildings - one even has a heated pool, depending on your budget you can get an amazing loft there!
In regards to commuting - driving over the bay bridge takes me about 30-45 minutes at 8:00 am - paying the toll CASH, if you leave earlier, get a fasttrak, it will be much faster. BART is just 2 stops from Downtown SF from the Lake Merritt station (which is 4-6 blocks from Jack London Area).