Aoi Hana aka Sweet Blue Flowers
This needs to be loved. So much feels for this one. A yuri anime that follows two childhood friends, Akira and Fumi, who become reacquainted during their first year of high school. Fumi is a lesbian who, at the start of the show, is recovering from a heartbreak. Adapted from the manga of the same name, it's a great adaptation that stays true to its source. There's great character development in this show, and is fairly realistic in its depiction. The art and music is gentle, well fitted for this show.
Ga-Rei Zero
I like to pretend that the manga it is adapted from doesn't exist, but I liked this prequel. This isn't that well known in Japan either, but episode 1 was fairly notorious as I recall. Of those that watched it, a common comment is that they wouldn't want to watch it again. Not because it is bad, but because it hurts to do so. Directed by Aoki Ei. It has decent action and great music too. Yomi <3
Strike witches
For all the hate it gets as a fan service anime, it has a really fun and likable cast. I sometimes wish they'd drop the stupid no pants thing so that more people would give it a chance, not for the story but for the characters.
Kyoukai senjou no horizon aka Horizon in the middle of nowhere
Again, despite its tendency to have some ridiculous boobs, it has a fun cast and world. Season 3 when?
Nodame Cantabile
I don't know how loved this is outside of Japan, but it should be loved.
Sabagebu
Great comedy. Would you believe it if I told you the manga it was adapted from is serialised in the shoujo magazine, Nakayoshi?
Saki
An enjoyable mahjong show where the characters are all ridiculously skilled, to the point where it's downright magic. Another show that has a huge cast and occasional boob fan service. Despite its huge cast, the show manages to make almost all of its characters, especially the opposing teams, memorable and likable. I would often find myself cheering for all sides in the tournament.
Some oldies:
Dennou Coil
Maria-sama ga Miteru
Kara no Kyoukai
Ichigo Marshmallow
Ouran highschool host club