I highly recommend Jiraishin; I once had a question about the protagonist after reading this manga: "why haven't he kill himself yet?". The manga itself is not a classic tragedy genre but more like distopia, action, seinen. The main character is the one guy who watches the world of people falls apart as he completes his missions. Then his own world also falls apart slowly. 5o5y21

The overall manga gives you a depressingly dark feeling that nothing can be done to make any it better. Usually, some sort of justice or revenge will give you a satisfying feeling in a normal tragedy manga. This manga will give you justice and vengeance but you won't good about it; in fact it makes you hate the world a bit more.

Not Simple?

I've read an unbelievable volume of tragedy stories. However, the most horrifyingly raw, gut-wrenching, real manga I've ever laid eyes upon is... a story about mountain climbing. Kokou no Hito might be just what you're looking for. The tone is solid throughout, but you have to wait a little while for the main character to get older, because that's when things really kick into gear. If you are hesitant because of the first couple volumes or the rock-climbing theme, try giving it a chance. It's one of the most awfully wonderful things I've ever had the honor to read.

It's seinen like ES and Bokurano, both of which I have ingested (in one form or another) and greatly enjoyed.

I hope this is what you're looking for. Good luck!

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Yuutai Nova is one of the most depressing things I've ever read..

Build up with the devastating loss...would Dear friends work?

Hmm...for seriously depressing, I nominate:
Deep Love - Ayu no Monogatari

The ones below aren't seriously depressing, but there is a bittersweet, melancholic note through out the story:
Hoshi no Koe (the anime version is called "Voices of a Distant Star")
Kon no Ki Konoha
5 Centimeters per Second (the anime is particularly stunning)

I also double-recommend:
Life
Vitamin
Watashitachi no Shiawase na Jikan (not outright depressing but still quite sad and bitterweet)
Oyasumi Punpun

I highly recommend the anime version of ef & the manga Mon Seul.

Also, H.O.T.D. & Ubel Blatt fit. Seikon no Qwaser (manga) comes to mind as well.

Aki-Sora & IO have a little comedy here & there, but most chapters are pretty deep (especially the ones about the past). Mama wa Doukyuusei does not fall from the serious side, either.

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Deep Love - Pao no Monogatari
T_T.. So sad.

Arigatou can be very depressing, especially if read in the wrong light. Otherwise an extremely dark comedy.
Believers
Koi Kaze
Freesia
Saikano the most depressing manga I've yet to read.
Lament of The Lamb

And since people are throwing out some anime too, I'll add to that with Now and Then, Here and There, and Texhnolyze.

Sarcasm just doesn't work over the internet.

Rainbow