San Fran is awesome if you want to work in the tech industry, but you better either know someone at one of the major players (Facebook, Twitter, Google, etc.) or you better get your masters degree or MBA from Stanford, Cal-Berkley or another top tier school. It's expensive and only getting worse. Culture is strong, resources are good, great nature is close by and running is solid.
Seattle is getting bigger and bigger, losing it's charm, becoming outlandishly pricey, but the job market is solid and offers you a lot of different routes to make a good living. Amazon is where I would try to work if I lived there. Running is okay, but you're close to BC, the ocean and mountains, so it's ideal.
Portland is where I decided to move. If you want to start a business, whatever it is, Portland is a great place to do so. People here live a lifestyle of doing what they want, not being defined by money. I swear most the people here work part-time and live life to the fullest. People are genuinely nice and support one another. There are plenty of homeless people, especially in the inner core, but there are very affordable housing options in up-and-coming neighborhoods. Running is on par with San Fran and Seattle and access to the ocean or Mt. Hood is all within 1.5 hours. From a cost of living standpoint it's more affordable and from a starting your own business standpoint it's the best place to try and start one (of the three options you laid out).