although best westerns arent by no means a luxury brand, the ones ive stayed in are better than your roadside BW motel. San Francisco Tuscan inn located just a block from the fisherman's wharf would be a good choice in a big city. When i stayed, they offered a wine and cheese reception and the rooms are small but nice. They dont offer a free breakfast but they do have a restaurant onsite. Although there are many options around for food.
Best Western Elm house in Napa is one of the best BB with outstanding costumer service and top notch breakfast. If you are looking for a honeymoon then napa is a great choice. You can also take the wine train and have dinner. The price for two its about 250 i think. There is also the Best western premier ivy inn which is bigger and more modern looking but the tripadvisor reviews made me want to go to the Elm house instead. Have not yet stayed at the premier.
The best western airport plaza in San Jose is really nice too. Remodeled rooms, great breakfast and staff. Though San Jose is not know for being a touristy place, its a good location if you want to take trips to Santa Cruz, Half moon bay, and San Francisco all with in an hour's drive