I've been going to the old Eagle Cafe for years, and have always enjoyed it. They recently re-modeled the restaurant, and it looks great. Windows all around, with views of the pier, alcatraz, coit tower...best of all, they revamped the entire menu, and the food is now amazing, and portions are huge, and well worth the price.
My boyfriend and I had the Crab, oyster platter, and linguini. Shared everything, and had to take more then half of it home...portions are BIG!!
While the wait for the food is a little more then your average restaurant, it's well worth the wait.
Pros: great food, great views, good service