I know this thread is ancient, but I thought I would search for this topic before I had decided to create a new one about it.
That being said, I just got done watching the last episode of Bebop again, and it really always gets me.
Then again, as pathetic and sad as this is going to sound.... I'm a complete sucker for inspirational and touching scenes in general... And have even teared up to scenes in Pokemon and Yu-Gi-Oh!
Only bawled my eyes out during Samurai X, though.