Legend of the Galactic Heroes (Anime) - Already recommended it to you, but I'll go in detail here. The series explores a vast array of themes such as war, politics, human nature, religion, etc. with a cast of some of the most well written and developed characters I've seen in fiction, great world building and great exploration of it's concepts.
Mobile Suit Gundam (Anime) - Already mentioned this before. If you like space operas, then most of the Universal Century timeline is worth checking out. The order to watch them would be Movie Trilogy, Zeta, Char's Counterattack, with the side stories of 08th MS Team, War in the Pocket and The Origin being good to check out after you've finished the movie trilogy.
Ashita no Joe - Easily the best sports or Shonen series I've read (or best manga overall, for that matter), with a good amount of stakes in showing the dark side of boxing that makes it essentially everything the first 5 Rocky films did but done hundreds of times better. It has one of the most well developed and memorable protagonists in manga, a rivalry only matched within anime/manga by that of Reinhard and Yang from LotGH and the most inspirational and engaging training segment in any series I've seen, not to mention having a perfect ending.
Battle Angel Alita - If you like fantastical sci-fi with a good deal of psychology, this cyberpunk manga is for you. The villains tend to increase not only in power scale, but internal complexity. The protagonist is one of, if not the, greatest female leads in fiction, the world building is complex and the amount of varied personalities and equalised perspectives between characters made the Zenith of Things Tournament found in the sequel Last Order the greatest tournament arc in manga by far. From what I've heard though, the 3rd part "Mars Chronicle" is shit, so you may want to just stop at the great ending Last Order provides.
Fullmetal Alchemist: Brotherhood - Pretty much a complete package when it comes to anything you'd want out of a story, be it a well developed cast who all have their role to play in the plot, a very balanced power system or good theme exploration on the topics of war, human existence or theology. Only real flaw I can think of is the Chibi comedy skits can be slightly immersion breaking, though not as bad as when most other series do them.
Rose of Versailles (Anime) - It was a slight inspiration for Miura, with Griffith's design and Casca's personality being primarily inspired by Lady Oscar. It's easily the best period drama in anime, with a some level of political intrigue (though nowhere near to the level of LotGH) and one of the few series along with Berserk to explore themes regarding gender roles without becoming Liberal
. Only real flaw to it is that the pacing of the early and mid episodes can be slow and some characters you'd expect to play a major role (eg. Louis XVI) do not.
Hunter X Hunter (2011 Anime) - Does everything good about Yu Yu Hakusho far better, be it story, character personalities/development, world building or theme exploration and doesn't have anywhere near as many asspulled power ups.
Hokuto no Ken - The general manly and detailed aspects of Berserk such as some elements of Guts' character may have been inspired by Kenshiro. It's a fairly simplistic story and can be somewhat cheesy at times, though it's one of the best you can find when looking for a fast-paced, action packed, violent manly manga brimming with 80s charm and featuring memorable characters.
Real - If you like Inoue's work such as Vagabond, Real is his best when it comes to the psychological examination of his characters and their struggles, with it's wheelchair basketball theme essentially making it a far superior version of Slam Dunk.
Will post some more later.