My favorite place in Kyoto is the Kiyo-Mizu Temple. It's up in the hills, so it commands amazing views of the Kyoto landscape. You can find it heavily referenced in manga (Ken Akamatsu's Love Hina vol. 3 and Negima Kyoto arc, and a few others come to mind), as "to jump from the stage of Kiyo-Mizu" is a common saying which means, "to do something with all your commitment." (You can survive the drop if you place yourself just right and throw yourself entirely into the literal jump). In winter, the Kanji character of the yer is housed there, and one can drink from the three streams that grant luck in health, wealth, and love. Also the way up passes through a winding row of stalls/stores, which are illuminated by lanterns, again making it very picturesque.
I know I sound like a tourism pamphlet, but this place really deserves a visit if you haven't been there already. I mention this place when chatting with Japanese, and they frequently agree with me and view me as well-traveled to mention Kiyo-Mizu.