Revolutionary Girl Utena is an Anime I discovered fairly recently, and it has quickly become my favorite Anime. For a very long time that title was held firmly by Noir, and I didn't think it possible any could take it.
It has a few themes in common with the Girls with Guns trilogy, a relationship between two girls that comes just short of being outright stated to be romantic, a confusing conspiracy, and even at times seemingly similar music (but not as similar as Madoka's). Also reflects Japan's French fetish. But these are girls with swords rather then guns.
However Utena also shares clearly relations to many more Animes as well, Rose of Versailles, Sailor Moon and Evangleion. And ChuChu gives it a little taste of Pokemon.
It also shares a great deal of what I love about Sucker Punch, but does it much much better. And it shares some themes with Pretty Little Liars too.
I'm not nearly smart enough to do an in-depth analysis, there are many online already. But I will likely be doing more Utena related posts in the future.