Hourou Musuko
Nausicaa of the Valley of the Wind
Voynich Hotel
Oyasumi PunPun
Aku no Hana
That's it. I will add some more if I can think of any. These were judged along three axes: Quality of art, quality of writing, and overall depth, which is predominantly influenced by writing, but art is important here too, such as the visual allegory of PunPun, or the imagery of Nausicaa walking among the feelers of the Ohmu.
And it has to have been completed, otherwise Bokura no Hentai would replace Hourou Musuko. Hell, I'm considering replacing it with The first thing I do in the morning is (fuck that title).