Meiji Jingu Shrine
Meiji Jingu has multiple entrances so plan ahead according to where you come from and plan to go after. We took the JR Yamanote Metro Line to Harajuku stop and entered through the giant wooden gate of the south entrance and exited through the north entrance to go visit Shinjuku Gyoen afterwards. Entrance to Meiji Jingu was free.
There is a long walk through a man-made forest to get to the main shrine and you will come across a small side entrance to Meiji Jingu Gyoen, where you can visit the Inner Garden, the South Pond, and a bunch of other sites. This part is not free but the 500 yen (~$5) entrance fee was reasonable. This paid area has two entrances too, one to the south (close to the south gate) and one to the north (close to the main shrine).