Lake Campbell Motel (1377 Hwy. 20, 360/293-5314, $55–105 s or d) is four miles south of Anacortes [1] along Lake Campbell. This is a good family place with microwaves and fridges in all the rooms; the more expensive ones contain full kitchens.
San Juan Motel (1103 6th St., 360/293-5105 or 800/533-8009, $55 s or $61 d, kitchenettes $65 s or $74 d) is a centrally located, clean place.
Anacortes Inn (3006 Commercial Ave., 360/293-3153 or 800/327-7976, www.anacortesinn.com [2], $90 s or d, suites $93–128) has rooms with fridges and microwaves, plus a seasonal outdoor pool.
Islands Inn (3401 Commercial Ave., 360/293-4644 or 866/331-3328, www.islandsinn.com [3], $79–89 d) has 36 comfortable motel rooms and suites ($140 d) with fireplaces, wet bars, and jetted tubs. An outdoor pool and hot tub are on the premises, and La Petite Restaurant offers gourmet dining, plus a complimentary Dutch breakfast. The owner is from Amsterdam.
Links:
[1] http://www.moon.com/destinations/washington/san-juan-islands/anacortes
[2] http://www.anacortesinn.com
[3] http://www.islandsinn.com