To add to the trifecta, I think there are a few more to mention:
Tatami Galaxy - This show is unique, but definitely thought-provoking. A lot of quick-talking, but if you sit through all of it, I'm sure you'll love it. Very satisfying.
Kara no Kyoukai - Garden of Sinners - It's a set of 7 movies that pretty much sum of what you liked. Very philosophical with a strong female lead that doesn't pander in the least. Great story and action.
Mushishi - This is another philosophical show, but it's slice of life as well. Contains a decent amount of fantasy elements.
Katanagatari - 12 hour long episodes that tell a very endearing story. A bit of romance, but very serious overall. It also has a really touching ending. Definitely not one to shy away from tragedy and some extreme choices.
Planetes - This is a show about two garbage collectors clearing trash in space. It sounds kinda lame, but it's an interesting slice of life show with a decent amount of sci-fi and another great female lead.
Blacksaber and Torillian also knows what's up. I think you'll enjoy the majority of what we've listed.