It would help if you gave more info such as how much time you have.
The Top 3 in Kyoto are the Fushimi Inari Shrine, the Kiyomizudera Temple, and Kinkakuji (Golden Pavilion). They are not near each other though so I don't recommend seeing all 3 back to back unless you're really short on time and dead set on seeing them all. Needless to say there are huge crowds of people going to them, so to have a better experience, since Fushimi Inari is open 24/7 it's better to go in the early morning or evening to avoid the crowds. Likewise, Kinkakuji starts to look like a morning rush hour train station from late morning, so entering as soon as it opens would be a good choice also. Kinkakuji will only take you 30 minutes without rushing, Kiyomizudera might take 60-90 minutes depending on your pace, and Fushimi Inari could take a couple hours to half a day if you want to run over all the trails.
One important tip - the main sights of Kyoto are its temples and shrines - if you have zero interest in such things, you can cobble together some other activities, but Kyoto might not be the best place for you. If you like them though, you could spend 8 months there and still not see all the city has to offer. But after seeing half a dozen places, your eyes might start to glaze over and they seem to become a blur - it is easy to get "templed out", so one key is to mix some variety into it all. There are some other good sights you could include - the Sagano Bamboo Forest, Murin-An Garden, Railway Museum, Iwatayama Monkey Park, Katsura Imperial Villa or Shugakuin Villa, Shoseien Garden, Nijo Castle, Nishiki Market, and other places can add some variety. For the villas, they are free but require a reservation - don't wait til a few days before or you may be out of luck.
For more ideas to fill up a day, try looking at the Japan Guide page and the Kyoto City tourism page.
And if you have the time, I HIGHLY recommend you make at least half a day available to see Nara as well. Most of the best is in the Nara Park area. Missing the Todaiji Great Buddha would be a tragedy. There are also many other sights there, like the Kofukuji Temple, Kasuga Shrine, plus Isuien & Yoshikien Gardens. Isuien is pricey but Yoshikien is free if you show your passport, so they both balance out.
Another excellent day trip is going to see Himeji Castle and the nearby Kokoen Garden. Absolutely stunning. Himeji Castle is the grandest and original surviving castle in the country - not a reconstructed fake. There are only a dozen originals left and Himeji beats them all.