Museums

• The Exploratorium (best museum ever)
• Musée Mécanique
• Magowan's Infinite Mirror Maze
• SF MoMA (not particularly unique, but I used to hang out in their cafe regularly and enjoyed it)

Landmark places

• Golden Gate Park
  • Moon Viewing Garden
  • Strawberry Hill island
• The Ferry Building
• Golden Gate Bridge

Nature/Parks/Walks

• Sutro Baths (regardless of whether you go here or elsewhere, be sure to see the cliffs)
• Dolores Park
• Twin Peaks
• Climb from the Embarcadero to Coit tower and up the tower

Columbus Ave:

• Specs' Twelve Adler Museum Cafe
• Vesuvio Cafe
• Mario's Bohemian Cigar Store Cafe
• Top floor poetry room at City Lights bookstore
• Bonus:
  • Caffe Trieste
  • Caffe Greco