Lain and Evangelion are my all-time favorites. I love the plots in both stories.
Speaking of plots, has anyone read the Prophecy of Tears?
http://tribes2.sierra.com/4_2_0_story.html
That's right. Tribes 2 actually has a plot!
Blake Hutchins is a really good writer, but he stopped writing once Dynamix closed. His little miniseries/chapters are better than most of the sci-fi stuff out in the market today.