I had a terrific two-night stay at Pacific Tradewinds Hostel. Their location in Chinatown is awesome, an easy walk from the piers after catching a ferry back from Sausalito. Their facilities are clean, their employees are friendly, and they offer the small perks that make hostel living easy and interesting. They provide storage (bring your own lock to avoid buying one) and they have a ton of showers and bathrooms. Make sure to book on their website to get the best rate and to save them from 3rd-party referral fees.