I researched this board before leaving on a week long trip with my 2 kids (one who lives in Seattle) and husband, heading north to Whidbey Island, staying in Anacortes, heading to San Juan Island, then off again to Vancouver. I feel like I owe a debt to the folks who report back following their experiences.
We were told that Toby's in Coupeville was great for mussles. Yep, I was the only one in our party to have them, and while they were good, this place doesn't allow anyone in under age 19. (Son is 18 and stands at 6'6", so we weren't questioned.) However, don't bother stopping if you have young kids. It was ok, but that is about it.
The Marina Inn in Anacortes was very pleasant. The 4 of us stayed there b/c the one closest to the ferry was full. My husband has spent many weeks up there for business, but had never stayed at this place. It was clean, just fine, and cost only around $80 for 4 adults! (a steal).
We enjoyed Lakedale Resort on San Juan Island. We've stayed at other places in Friday Harbor on trips when we didn't have a car, but this time we decided to try something between Roche Port and Friday Harbor. We stayed in a log cabin and it was LOVELY. It's costly, but remote (NO cell phone svc, no internet) and this is SO RARE anymore, but it was such a blessing!!
Sorry not to report more on the restaurants. We did indulge in lunch at the Market Grill in Pike's Mkt for salmon (or shrimp) sandwiches. Delicious!! (thanks for the recommendation. Problem is: there are like 10 bar stools, and if you can't get them, you need to carry your lunch out to somewhere else to eat. I bought the salmon for $ 29.99 at the first fish mkt you walk into, (smoked on alderswood or some such) and loved it so much I carried a cooler around with me the entire time and snack on it constantly. This is some seriously tasty smoked salmon.
One last thing: we hiked all around Friday Harbor looking for a good lunch. Picked a place called "The Market" and it was REALLY good. My kids ordered off the menu and loved their sandwiches, I loved their prepared salad bar, which was loaded with interesting items that you could taste before ordering. Most local folks seemed to jam this place.
Thanks for others reporting in; you made our trip more memorable!!