A whole bunch of Terry Pratchett's Discworld series. And many of the ones with male main characters have a strong female supporting cast. I'd recommend Monstrous Regiment to the uninitiated.
Most of Isobelle Carmody's books but most of all the Obernewtyn series.
The Artemis Fowl books have a female co-lead.
Those are the first to come to mind.
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Spending as long as I do here, it's easy to forget that Oddworld has actual fans.
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