In more or less random order (love them all) and being far from complete:
Female o Ellen Ripley (Alien) o Pvt. Vasquez (Aliens) o Motoko Kusanagi (Ghost In The Shell) o Trinity, The Oracle (Matrix) o Maude (Harold and Maude) o Weronika/Véronique (The Double Life of Veronique) o Amélie Poulain (The Fabulous Destiny of Amelie Poulain) o Kaylee (Firefly/Serenity) o Galadriel, Eowyn (Lord of the Rings) o God (Dogma) o Beatrice (Much Ado About Nothing) o Idgie Threadgoode (Fried Green Tomatoes) o Ivanova (Babylon 5)
Male o Captain Jack Sparrow (Pirates of the Carribean) o Batô (Ghost in the Shell) o Hannibal Lecter (Silence of the Lambs) o Indiana Jones (Raiders of the Lost Ark, etc.) o Harold (Harold and Maude) o Aragorn, Gandalf, Gimli, Boromir, Pippin, King Theoden, Witch King/Gothmog, Denethor, Eomer, Grima Wormtongue, The Mouth of Sauron (Lord of the Rings) o Han Solo, Yoda, Darth Vader (Star Wars) o Mal and Jayne (Firefly/Serenity) o Jake and Elwood Blues (The Blues Brothers) o Dominar Rygel XVI (Farscape) o Silent Bob and some other characters whose name I forgot (Dogma) o Brian and some other characters I don't remember by name(Life of Brian) o Benedick (Much Ado About Nothing) o William Wallace (Braveheart) o Capt. Jack Aubrey and Dr. Stephen Maturin (Master and Commander) o Damiel, Cassiel and some others(Wings of Desire) o Scrat (Ice Age) o G'Kar, Londo Molari, Garibaldi, Vir (Babylon 5)
I know I forgot tons of intriguing characters but hey it's a start...