The actresses who've logged the most time with the prolific writer/director are...
1. Mia Farrow -13 features.
Remarkably (and horrifically) despite the plentiful acting nominations earned by Woody Allen films she's still never been nominated.
2. Diane Keaton -7 features
including her Oscar win for Annie Hall
3. Julie Kavner -"Marge Simpson!" 6 features
most memorably as his co-worker in Hannah and Her Sisters
4. Dianne Wiest -5 features
including both her Oscar wins for Hannah and Her Sisters & Bullets Over Broadway (If you've ever wondered why actors are so obviously desperate to work with him, consider this: He's guided thespians to 14 nominations with 5 wins among them -one of the best records of all time.)
5. Louise Lasser -5 Films
including Woody's first: What's Up Tiger Lily (1966) if you count voice work.
6. Judy Davis -4 Films
including her Oscar nominated turn in Husbands and Wives
7. Blythe Danner, Julie Halston, Annie Joe Edwards and Camille Saviola -3 Films (character roles)
8. Scarlett Johansson -soon to be 3 Films.
Even if you discount the actresses who never had prominent roles, Scarlett would still be in only 6th place.
9. A lot of actresses with 2 films including:
Charlize Theron, Debra Messing, Lynn Cohen, Tracey Ullman, Mariel Hemingway, Julia Louis Dreyfuss, Joanna Gleeson, Anjelica Huston, Marian Seldes, Gretchen Mol, Tina Sloan, Erica Leerhsen and Loretta Tupper... possibly some others, too.