Depends on what you are looking for. Turtle Tower has the best Pho Ga (chicken noodle soup) in the City, IMO. As mentioned above Bodego Bistro is very good for a sit down dinner with various entres like Shaking Beef. Siagon Sandwich is the standard for Bun Mi.
Turtle Tower Restaurant
631 Larkin St, San Francisco, CA 94109
You will probably want to do a search of this board to get the recommendations and feedback of locals on the multitude of Vietnamese options in this area but we really enjoyed our visit to Bodega Bistro. They had the best version of bo luc lac (shaking beef) I have tried, and the papaya salad was also very tasty. Decent pho bo also...
607 Larkin St, San Francisco, CA 94109