I also agree that it's easy to get "templed out". I'd pick a few that you think you must see and drop others. I wouldn't bother with the Imperial Palace tour - I found plenty of things much more interesting around Kyoto.
That said, there is one temple that I rarely see get mentioned and yet I find more fascinating than just about any of the others: Otagi Nenbutsu-ji. You'll find over 1000 rakan statues (some of which are quite humorous - such as a tennis player) throughout the small grounds. It's in the northwest part of Arashiyama, and the bus that goes up to Kiyotaki (#67?) stops there. There is a nearby tunnel that leads up to Kiyotaki and some of the locals say that you will see ghosts should you choose to walk through it.
Also if you are into nature, I think the Bamboo Forest (also in Arashiyama) is worth a visit. If you can go early in the morning you'll find the light very pleasant for photography and very few people around. I visited it just a few days ago at about 7:30a and the only people there were two other photographers, so we were careful to stay out of each other's shots.