When I think of a "coffee shop" places like Sambo's, Perko's, Zim's, Denny's and other unique local establishments come to mind. A place that serves simple reasonable priced fare with breakfast available 24hrs. They had 2 kinds coffee - regular and decaf with the orange rim. With this definition I have a few local favorites.

Lucky Penny - This is the last "survivor" of the Copper Penny chain. It's essentially the same thing with a different name.

Pinecrest - If you are in San Francisco be sure to stop in and have the Eggs Benedict or Florentine - any of the poached egg dishes are delicious! But be aware, they are not on the menu - it's a "locals only" type of deal. Like getting a burger "animal style" at In n Out.

Not local but definitely a favorite...

Denny's - It's 3AM, you're fucked up and we're open. 'nuff said.