Strong heroines with a good plot, eh... I can think of several, though they're all seinen/shounen, but don't let that deter you. All of these are very good.
The "if you haven't watched this already, why aren't you watching it right now?":
Steins;Gate (drama, sci-fi)
Angel Beats! (drama)
The less appreciated:
Mawaru Penguindrum (comedy, drama) has as much as symbolism as a English class book, except it's actually entertaining.
Jinrui wa Suitai Shimashita (comedy, slice of life) is hard to describe and doesn't have much of an overarching plot due to the genre, but it's a very unique and underappreciated anime.
Seirei no Moribito's (fantasy) main lead puts most shounen battle series to shame. One of the best characterization of a strong female lead that I've seen in anime, if not the best.