Longer than 26 episode "dark" series are very few and far between. Most run the 26 episodes, give or take.
ERGO PROXY - I never got particularly far into it, but it is one of the dystopian, post-apocalyptic series that you are looking for. Runs 23 episodes.
Gungrave - Story begins as a monster story, flashes back to a mobster story, and then returns to its dark roots as a monster story. Good action, the flashback has an excellent plot, and it runs 26 episodes.
Berserk - Again, monster story, medieval flashback this time, return to monster story. A true classic, excellent dub if you don't mind them, and all the darkness you can handle in a plotline. I believe you are familiar with this title, but it runs 25 episodes.
Chevalier D'Eon - French period mystery at its finest. Not to my particular tastes (delays in subbing combined with the slow plotline at the time forced me to drop the series). However, the series has fantastic music, excellent animation if you grab the HD subs, and a dark, vaguely satanist plotline. Zombies, possessions, and plenty of that fun stuff. Runs 24 episodes.
Gantz is up the alley you're looking for, but make absolutely sure you get DVD rips for the first half of the series, that part was censored on television. If you like it enough, but aren't so sure about the ending, read the manga instead up to the "Second Phase."
Noein - Don't be thrown off by the simple art. This series is a lot more deep than it appears. Sci-fi, dimensional travel, and darker undertones. Runs 24 episodes.
RahXephon - Towards the darker side of mecha without going emo (Evangelion), you will find RahXephon. Post apocalyptic, violent deaths, last hope of humanity. Look no farther. Runs 26 episodes, accompanied by an excellent musical score.
SaiKano - Alright, this series is only 13 episodes. You want dark, depressing, tragedy? This here would be the pinnacle. The be all, end all, lord on high of dark anime.
Bokurano - Can't say I've seen it, but this would be another darker series. Children in mecha, add in a bit of despair, and a high price for victory. Runs 24 episodes. I've heard the manga is even darker, and edits were made to the story.
Mahoromatic (seasons 1 and 2) - Billed as a comedy. Why is this a "dark" series? Could be due to the fact that every single episode ends with the exact number of days the lovely automatic maiden has left to run before she dies. Don't let the humor deceive you. 26 episodes total.
Basalisk - Ninjas, blood, gore, tragedy. In a fight to the death between families, there are no winners. 24 episodes total.
Witch Hunter Robin - Dark visuals, dark concept, another dark anime for this list. The title is fairly self explanatory, and the visuals are nice. I loved the OP/ED, and the music was also good. Runs 26 episodes.
Lastly, there is Monster. The only series in my suggestions that matches your criteria. 74 episodes total. Murderers. I don't know much else, but this series is loved by many who have seen it.
Now, if you want manga, I can provide that as well, there are plenty of those.