Start your day at Calico Cupboard Café & Bakery (901 Commercial Ave., 360/293-7315, 7:30 a.m.–3 p.m. daily) for great homemade country breakfasts and healthy lunches. Save room for dessert: The fudge pecan pie and apple dumplings are legendary. Get there early on weekends, or be ready for a wait.
Let your nose lead you to La Vie en Rose French Bakery (418 Commercial Ave., 360/299-9546, www.laviebakery.com [1], 7:30 a.m.–5:30 p.m. Mon.–Fri., 8 a.m.–5:30 p.m. Sat., closed Sun. except in July and Aug. when open 10 a.m.–4 p.m.) which bakes warm French pastries and breads, while stirring up delicious soups and sandwiches for lunch. If you're heading out on the ferry, have them put together a box lunch special.
For food with a side of sass, stop by 
Gere-a-Deli (502 Commercial Ave., 360/293-7383, www.gere-a-deli.com [2], 7 a.m.–4 p.m. Mon.–Sat., closed Sun.). This funky little eatery offers cleverly named (and tasty) sandwiches, salads, soups, and homemade desserts. Munch away while enjoying the antique signs and advertisements lining the walls here.
Links:
[1] http://www.laviebakery.com
[2] http://www.gere-a-deli.com