Hi nassen, this is a theme which shows up in a lot of excellent publications. As far as e-novels I'd suggest "The Chronicles of Soraya Blackheart" by Munchausen, a fantasy tale about a truly strong woman which also happens to be illustrated by FTKL.
As for e-comics, one of my favorites is the sci-fi epic "Vicky's Defeat" by Scavenger, which definitely fits the bill for a strong female protagonist/villain.
These are only examples. There are lots of other great ones out there!