A few books that pay back the time spent on them before or during a Kyoto trip.
For a single readable introduction, Kyoto: A Cultural and Literary History by John Dougill (Signal, 2006) walks neighbourhood by neighbourhood through the city's history and literary associations and is a good companion in the field.
On the geisha quarters, Liza Dalby's Geisha (University of California Press, 1983) is the classic anthropological study by the only Western woman ever to train and work as a geiko in Kyoto. Mineko Iwasaki's autobiography Geisha, a Life (2002) is a corrective to Memoirs of a Geisha by an actual former Gion geiko who served as one of Golden's sources before publicly disowning the book.
For temples and gardens, Marc Treib and Ron Herman's A Guide to the Gardens of Kyoto (Shufunotomo, 1980 and various updates) remains the best single-volume garden guide. Donald Richie's A Tractate on Japanese Aesthetics (Stone Bridge Press, 2007) is short, idiosyncratic, and changes how you look at a moss garden.
For history, The Tale of Genji by Murasaki Shikibu, in either Royall Tyler's or Dennis Washburn's translations, is the eleventh-century novel set in the Heian court of Kyoto and is the closest you can come to inhabiting the city's earliest imagined world.
For atmosphere, JunichirÅ Tanizaki's The Makioka Sisters (set partly in Kyoto in the 1930s) and his essay In Praise of Shadows are still the best literary preparation for the visual mood of the city.