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Below is a list complied of 67 female characters who were sexually assaulted. (Actually, it's less than 67 because some of the things they listed are most definitely not sexual assault, and I've noted those instances when I spotted them.) The list was an attempt to document how often rapes occur in comics. Apparently, they’ve be working on it for about 7 years now.
Abby (Ref Needed)
Alicia (Fantastic Four #255) Implied
Arella (Raven’s mother)* Even though we might consider Trigon disguising himself as a real man false pretense, Arella did seem to be aware that she was “marrying” an extradimensional being/demon, so that gets a little iffy as rape.
Arisia (Warrior #42) Implied
Atlanna (Incest, Atlantis Chronicles)
Aurora* (Supposedly raped by Sabertooth in Weapon X)
Barbara Gordon (The Killing Joke) Implied
Big Barda (Action Comics #592-593)
Book, Mallory* (She-Hulk, seduced by Andy’s Starfox powers, false pretence)
Boom Boom* (suggested on the boards that she was raped by Kilgore)
Calliope (Sandman)
Carol Danvers/Ms. Marvel (Avengers#200)
Cassie Sandsmark/Wonder Girl (Statutory, TT Annual #1 -- Age?) This was not rape. When both people are underage, it isn’t rape.
Catwoman (Her Sister's Keeper)
Cobweb (TS#1) Implied
Cora (Atlantis Chronicles) I haven’t read the book, but my research suggests this was actually consensual incest.
Crazy Jane (DP)
Dazzler (False pretenses, Longshot's luck power, ref needed)
Debbie Darnell/Star Sapphire (JLA #115) Implied
Diana/Wonder Woman (WW#10& 51)
Dinah Lance/Black Canary II (GA: The Longbow Hunters) Implied This is disputed by Mike Grell who wrote and drew the scene.
Dream Girl (Universo Project) Implied
Elektra (Daredevil #181 Implied, Elektra: Assassin #1)
Emma Frost (Ref Needed)
Engineer/Angela Spica (The Authority #21, 27)
Felicia Hardy/Black Cat (SM/BC mini)
Grace Choi (Outsiders #17)
Hawkgirl (Hawkman, ish # needed)
Helen Bertinelli/Huntress (Huntress miniseries ??)