Fidalgo Country Inn
I believe that the price was in the 80 to 90 US dollar per night range. I can't compare Fidalgo Country Inn to the other motels in Anacortes because I haven't stayed anywhere else in recent years. However, I've spent about five weeks at this inn over the past year and a half (mostly during 2001), and I've always had great experiences there. The rooms are clean and comfortable, and the staff is excellent. I've joked with them that when I get married, I may honeymoon there because the place is so pleasant.
The only real disadvantage to Fidalgo Country Inn is that one must drive a few miles to reach Anacortes. The location was very convenient for my work, but I could see some advantage to staying closer to town if I were a pure tourist. Anacortes doesn't have many restaurants in the main 'town' area, but being able to walk to them from my motel would have been an advantage. There is one restaurant/bar within very easy walking distance, so even this disadvantage is mitigated.
Having dispensed with the disadvantage, I'll mention some advantages. Many of the rooms are off hallways with security access doors. While I've grumbled a few times at having to dig for my key just to get into the hallway on a cold night, I recognize the value of this security measure. The inn provides a continental breakfast from 5:30 to 9:00 every morning. This breakfast isn't just stale doughnuts and cheap bread next to a toaster. They have all kinds of pastries, bagels, and cereal. They also have fresh fruit for those who are more health conscious than I am. Again, the biggest thing that I liked about staying there was that the staff was so nice to me.
Fidalgo Country Inn is located on Hwy 20 and is a good place to start on all kinds of adventures. The few miles distance between FCI and the town will make no difference in catching a ferry for a trip to the San Juan Islands. A quick right turn from the parking lot starts you on your way to Whidbey Island. I often came home from work, changed shoes, and fifteen minutes later was hiking at Bowman's Bay or Deception Pass State Park. FCI is about fifteen minutes from Skagit Valley, and I strongly recommend it to anyone visiting the area in June to see the Tulip Festival.