So I just watched episode 9 of Yamato 2199, "A Clockwork Prisoner" and I want to write down my thoughts on it real quick.
This is probably my favorite episode so far in terms direction. While the themes of "can robots have feelings," and "what does it mean to be human" have obviously been done to death in these kind of stories and there's not really much to take away from them anymore, this episode does an awesome job at establishing and maintaining a mournful and frantic tone that really makes the episode for me. Speaking visually, there are a few absolutely gorgeous and eerie shots at the end with Analyzer standing on the bridge of the Yamato against the backdrop of a star. There's also some pretty cool cuts to a radio dial while everything is being wrapped up and book-ended.
The thing that really made the episode was how Alter was characterized though. He was inarticulate and like a child. In a lot of these kind of stories, like Blade Runner for example, the robots are designed to be human, they're very communicative, and you get the feeling they're trying to convince the other characters that they're more than just circuitry and programming. Here, it's the opposite. There is not a question of subterfuge. We don't get much, other than the sense that Alter is trying to make sense of things. He never tries to justify his existence to the viewer and during his escape, he's just frantically moving forward leaving the other characters to fill in his motive.
Combine this with the composition of the episode - the music, all the little cool shots, the whole "friend" thing in Alter's task logs, and the "Heart of Observer" parable that's related throughout the story - it was an episode that really left an impression on me.
/end fanboy