I'm going to throw this up here and people can do with it what they will...
Orphan Andy's
2370 Market St at Castro and 17th
Serves 24 hour breakfast and diner food. Take any train to Castro station. It is right there. This place is not for everyone, but it is San Francisco beyond the safety of the Wharf and downtown. If a burly man in a kilt is not your thing, well don't come here. Good food, and a great scene, especially at 2:30am. Enjoy!
Also another thumb's up to Tartine