My absolute favorite place to stay along this route is in Ashland (Oregon). It's just north of the California border dividing your drive nearly in half. The town is beautiful, charming, and has a lot of character. Known for the Oregon Shakespeare Festival, it's also home to quite a few great restaurants including the Liquid Assets wine bar and restaurant. I love the bacon wrapped dates there and they do a nice duck dish as well. I've stayed at the nearby Best Western Bard's Inn which is economical, but very clean and offers a decent breakfast. I've also stayed at the BEAUTIFUL historic Ashland Springs Hotel which also offers a decent breakfast and has beautiful rooms. The adjoining Larks Home Kitchen Cuisine is excellent. If you have time and the season is right (not raining), you can enjoy a break from the car by perusing Main street full of cute little shops and cafes. Explore Lithia Park and, if you're daring, try the local "Lithia Water" that comes up from fountains in the park. It's full of minerals and thus, not quite as delicious as normal water.
I've driven this route probably 20 times. A Greyhound once and even hitchhiked it. Thanks for bringing up some great memories. I'd agree with Ashland (Oregon). Give yourself an hour or two to poke around; it's interesting. I recall some high quality arts and crafts there.