Oh, I guess that Shadow Star Narutaru and Alien 9 would also qualify, but neither of them is actually all that good, imo.
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Revolutionary Girl Utena is incredibly good, but I still don't understand people calling it a magical girl show. Like, sure it has a transformation sequence and a fight of the week, but the rest of the tone and structure of the show has far more in common with shoujo shows that /aren't/ magical girl shows. Definitely watch it regardless.
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Or maybe what made you actually like Madoka wasn't it's genre, but was it's creative staff. In that case, if you're looking for something with a similar overall audiovisual feel, try Le Portrait de Petit Cossette, which has the same director and composer. If instead it was the writing that pulled you in, give Fate/Zero a try.