Some places really make an effort with their manhole designs. Yuda Onsen in Yamaguchi with more than 30 different designs being an obvious choice (click here for some examples). Another place I recently discovered is Beppu, the famous hot-spring resort in Oita.
The first one features Cosmos (kosumosu) and Rose Mallow (Fuyou)
Crape Myrtle (sarusuberi) and Sunflower (himawari)
Plum (ume) and Daffodil (suisen)
Wintersweet (loubai) and Pot Marigold (kinsenka)
Bush Clover (hagi) and Canna Lily (kanna)
Peach (momo) and Pansy (panji)
Hydrangea (ajisai) and Daisy (maagaretto)
Another post later as this is not all the ones I found in Beppu.