animê recommendations?

A bit of warning that milage may vary on this as there are some here I did not enjoy and some are a bit borderline about whether or not they contain what angel Beats had that you didn't want, but you should be able to find something that fits your criteria.

AKB0048
Ano Natsu de Matteru
Denpa Onna to Seishun Otoko
Gedo Senki
Hanasaku Iroha
Ikoku Meiro no Croisee
Inu x Boku SS
Karigurashi no ArrietyKuragehime
Lovedol: Lovely Idol
Mayoi NEko Overrun!
Omoide Poroporo
Ouran Kouhou Host Club
Sakamichi no Apollon
Shining Hearts: Shiawase no Pan
St. Luminous Mission High School
Summer Wars

Well I think FMA fits that descrição pretty well since it has one of the best story lines in all of mankind but you said "non mainstream"...
Maybe Tsubasa Chronicles?

Well, some I think you may like are
Myself; Yourself
-This series is very realistic and tackles real life problems as well. The animation is not the best, but it is a very good series, neatly packed into 13 episodes, and the ending, I find to be quite satisfying.

Kanon 2006
-It is a KEY series, so it will be heartwrenching at some scenarios, but the ending is no geral, global good, the characters are all very well developed, and the plot itself is very unique in my opinion.

The Melancholy Of Haruhi Suzumiya-
It is a very fun series. Very random, but it does have hints of romance in it, especially in the movie. You might consider this series mainstream and might have already seen it, but if you haven't, try giving it a shot.

Ano Hana-
This series is quite sad, probably not as sad as angel Beats! But still coração wrenching. It is only 11 episodes, so not so long, but I think it is a good series.

Shuffle!-
Depending on what girl you like the main male of the series to be with, you may or may not like the ending. The characters all have well developed back stories (The one I find to be most developed is Kaede) and all have serious moments through out this comedy harem. The ending, like I said, may or may not please you. I thought it was the best way to end the series, but I would have liked to see the other possible relationships as well. Over all, it is a good series worth watching.

Omamori Himari-
This series is an ecchi action comedy, but does have touching scenes and amor able characters in my opinion.

Blassreiter-
This series is an action series but it does have very touching and coração breaking moments also. The main character is very well developed and the focuses of amor and family are themes playing a part in the series as a hole. The ending, in my opinion, is no geral, global happy and the series in general I give four stars out of four stars to.

Hope you like them. :)

Mahou shoujo lyrical nanoha- its awesome,cute girls,and touching happy ending!its different from other magical girls,i'm totally loved it! (picture)

mashiro iro symphony-cute anime,with bit harem romance

hyouka-cute,sweet,nice!

guilty crown-cute girls,happy ending bud have sad side too,its have action and romance.

idk, maybe:
A Certain Scientific Railgun,
black rock shooter (pic),
the girl who leapt through time
Hanbun no Tsuki ga Noboru Sora
ef - a tale of memories
anohana (not sure about this, i cried almost the entire serie trought)
clannad, maybe :-p

Steins; gate and Madoka magica sound right up your street! Both have great characters, intresting plot, plotwists, sad parts and an awesome end!

Kara no Kyoukai, Code Geass, and No.6 are perfect!!!! They have some very serious subjects as main plot points, and the stories are all touching and deep. Code Geass can be a little sad, but mostly they all aren't so tragic.