Hi,
The pass is most effective for long distance travel. It's of limited benefit in the cities, and you cannot use the pass for city subways.
In Kyoto you can go to Arashiyama from Kyoto Station or down the Nara Line to see the Fushimi Inari Shrine, Uji, and of course, Nara. In Arashiyama there are many good places too, including the Tenryuji, Gioji, Adashino Nenbutsuji and Otagi Nenbutsuji Temples, the Iwatayama Monkey Park, bamboo grove, and many more good places.
Around Tokyo the main use is on the Yamanote Line, which goes to many popular places. For Osaka, there is the Loop Line.
Good luck.