Colorful manhole covers with animation characters or other objects with connection to the locale is another "Only in Japan" thing. I've put together information of manholes that are centrally located in Tokyo.
Sumida Ward - Nearest station: Ryogoku Station (JR Sobu Line or Toei Oedo Line)
Ryogoku is known as the town of sumo and also the birthplace for Katsushika Hokusai, the ukiyo-e artist known for woodblock print series "Thirty-Six Views of Mount Fuji".
Taito Ward - Nearest station: Ueno (JR Lines, Tokyo Metro Ginza and Hibiya Line)
There are two Pokemon-themed manholes inside the Ueno Park, one next to the National Museum and the other next to the National Museum of Science and Nature. Both are to the left side of the main entrance.
Chiyoda Ward - Nearest station: Ochanomizu (JR Chuo and Sobu Line), Jinbocho (Hanzomon, Mita, Shinjuku Line)
There are three manholes themed on characters from Osamu Tezuka's "Astro Boy" manga series. The name Professor Ochanomizu is taken from this area, and Astro went to Ochanomizu Elementary School. They are all on Meidai-dori, the large street that runs south in the direction of Jinbocho, the district known for its used book stores.
Shinjuku Ward - Nearest station: Shinjuku (JR/Tokyo Metro/Others)
There are two Godzilla-themed manhole covers in front of the Shinjuku Toho Building which contains the Hotel Gracery and the Godzilla head on the corner of the tower.
Along the Odakyu Line
The Odakyu Train originates from Shinjuku and extends all the way to Hakone Yumoto. There are three stations along this route that have a concentration of special manhole covers including Machida with six Pokemon-themed covers.
MACHIDA STATION, 30 minutes by a rapid express train from Shinjuku. Another 10 minute walk to Serigaya Park 芹ヶ谷公園 where all the manholes are located. Access to park will require going down long stairs.
TAMA CENTER STATION, 40 minutes from Shinjuku on a Tama Line express line, a route which branches off the main route at Shin-Yurigaoka. Also can be accessed on the Keio Line, a different company train that also originates at Shinjuku.
This is the center of the Tama New Town residential area and also home to Sanrio Puroland, the theme park dedicated to Hello Kitty, My Melody and other kawaii characters. There are several versions of the Hello Kitty manhole near the Puroland and around the Tama Chuo Park south of the station.