[samokan]

In Kyoto:
Hien Shrine - for me the best time to visit is during spring, the
flower ( cherry blossoms ) will be in bloom that time.
Otemon ( the big gate ) - the gate looks like a very big yen symbol , the name actually mean the "big gate"
Arashiyama - love it there especially during autumn and spring
Fushimi Inari Taisha - if you have seen the movie "Sayuri" or "memoirs of a geisha", this was the temple were she ran , the one with lots of gates.

Himeji area:
Himeji Castle -
Mt. Shousha - great area, like you were in old Japan. Here u can find temples , very old temples and resting place of the imperial family ( i think it was the Honda family ). This was also one the location for the movie "Last Samurai "

Mie -Ken
Ninja Village - in Iga-Ueno. dress up like a ninja and visit a ninja house.