One of the anime I find underrated is Saiunkoku Monogatari.
A Reverse Harem Shoujo Anime at first sight, a very good Shoujo Anime at second.
Atypical Heroine, Kou Shuurei tries to find her way Saiunkoku's political world, ruled by men. Yes, many of the guys like/love her, but she rejects them all. 8D Which is part of her charm, really... and Ryuuki's attempts at getting closer to her are hilarious at times...
But that's not all there is to it. Based on the unfinished series of light-novels by Sai Yukino, this Anime has a very strong cast. Each character is well rounded, has their past, their reason to act the way they act and more. :3
Yes, yes, I love this (so far) two seasons counting (2x39 episodes) anime.
Too bad the fandom is so small. D: Maybe the novels might be translated then...
Another anime/manga is Candidate for Goddess by Yukiru Sugisaki (DN Angel's Author). It's unfinished (*cries*) but it's very good for a Mecha series... i don't like Mecha, I seriously don't. But the cast was very good... And I really want to know how it ends. DX
Let's see, what else...
Oh, yes.
Pretear is a shoujo (magical shoujo), but a very good one. Not too sweet, and a strong story line. With only 13 episodes, it's not too long and void of filler episodes. =)
I don't know if it's underrated, but I haven't heard much of this series: Seirei no Moribito (Guardian of the Sacred Spirit)
It's very good with a very special artstyle... and backgrounds are amazing. o3o
Very nice story as well. ^_^