After two visits I still only have seen a fraction of all the temples in Kyoto. Most remarkable are the big differences between them (probably caused by the fact that they were built during several periods within the long heydays of Kyoto).

For a first-time visitor I would recommend Ginkaku-ji (the Silver Pavillion), Ryoan-ji (to sample a fine Zen garden) and Daitoku-ji (no worldheritage status, but a lovely complex to walk around).