My top 3 is pretty mainstream:
1. Neon Genesis Evangelion
2. Cowboy Bebop
3. Ghost In The Shell: Stand Alone Complex
I think I've explained my preference for these three shows elsewhere on the forum... but I'll repeat it here in short: Ghost In the Shell: SAC is just fine for the themes it explores on the subject 'What is identity?' and how it speaks about the line between man and machine, organics and technology, the brain and computers. Aside from that, it features great action, and even if not all the characters from the Section 9 team are fleshed out in an equally elaborate manner, the main ones (Kusanagi, Batou, Togusa) are very compelling.
Cowboy Bebop is awesome because the main characters basically AREN'T heroes. Yes, they do very heroic things in each episode, more often than not out of a true sense of justice. But what I like is that their motivation is not to be heroic, but simply to collect their bounty as bounty hunters, so that they can eat another day. It's like watching real people, with real-life problems, even if they are bounty hunters on a space ship. In that regard, it reminds me of Red Dwarf, though the main characters in that aren't bounty hunters. Also, again, the action scenes in this one are CRISP! That goes for the space battles as well as the hand-to-hand fights and shoot-outs. And last but not least props to Yoko Kanno for the great soundtrack.
Neon Genesis Evangelion.... I just recognise sooo much of myself in the main characters. Rei is almost exactly how I used to be as a teenager. I love the Shinji/Misato relationship. I love the story and the course it runs from start to finish. I think both the final two episodes, and End Of Evangelion are beautiful, if unconventional. I just have mad love for Evangelion.
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clarity of thought before rashness of action