If you liked
Shinseiki Evangelion
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...then you might like
M3: Sono Kuroki Hagane
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What M3 does Neon Genesis Evangelion did before it and better. That being said, M3 has more characters and group dynamics, which is a worthy addition, while NGE was about loneliness, abandonment, and how they shape people and their choices. On the other hand, while NGE's characterization is better and there are proportionally more adults, there are few "likeable" characters; M3 is a more typical genre anime with a larger cast with plenty of cliches which makes it easier to find someone to like. If this is an essential element for enjoying anime, Neon Genesis Evangelion might not be a rec for you.
If you liked
Narutaru: Mukuro Naru Hoshi Tama Taru Ko
|
...then you might like
Milk Closet
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Both are cute, but dark, and depict a particular kind of violence. Narutaru is deeper, has more mature themes, and is more focused on interactions. Milk Closet is more straightforward and the children are younger so several issues from Narutaru don't feature here at all.
If you liked
Alien 9
|
...then you might like
Milk Closet
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Both are about a team of small children that partners with "aliens" to fight other aliens. Both are darker than expected at first glance. In both the main female character is the most reluctant, but Milk Closet has a lot of twists later on.
If you liked
Hikaru no Go
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...then you might like
Shion no Ou
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Roughly the same theme. Where Hikaru no Go is about go and, after awhile, the professional world of go, Shion no Ou is about shogi and the pro world of shogi. They also have very young protagonists, though Hikaru is just starting out, while Shion is already an accomplished player when the series starts, so Shion no Ou has less of an underdog theme.