As mentioned, Fishermans Shack is a fantastic little bait shop, they have a good web site, too: www.fishermanshack.com.

Fishermans corner is a pretty good place, he is 2 blocks from my house, but he is not open as often as I would like to see. He is also out of bait as often as not.

On the coast, the best I have seen hands down is Harry's Bait and Tackle, a little old shop with rock solid information, and good prices. They are on the Bayfront in Newport.
Sweet Home-Dandee's is pretty good.
Lebanon-Ricke's is pretty good, good guns too.
Prineville- Prineville Sporting goods
In Alsea, there is a store on the right as you are headed west, I can't remember the name.

Sorry to the good shops I have forgotten, I will repost as my memory unfogs.