People are talking about Hurricane Kates in oldtown, haven't tried it myself. Lunas has good dine in Mexican. Tomasos for decent informal italian. The Marina at woodley island is not bad, with nice view of harbor. Order the fresh fish. I would avoid both the brewpubs for food. The Fresh Freeze has great burgers and shakes. I've heard good things about The Sea Grill, haven't been there either. The Rib Room at the Eureka Inn has nice atmosphere, the food seems to vary year by year. Denis and Jeris in Myrtletown have inexpensive family style italian meals. In Arcata there is Abruzzi, upscale Italian and all the college town snacky fare.
The Samoa Cookhouse is worth doing once. Lumber camp style Breakfast, Lunch and Dinner. Go for Breakfast.
Also Try : http://www.humboldtdining.com/