As of today, May 18, 2013, from Comic Vine site.
Storm from Marvel Comics, is number 1 with 5,225 appearances in comics, despite of appearing later than the other female comics characters in the top 5.
The Top 5.
1. Ororo Munroe aka Storm from Marvel Comics: 5,225
First Appearance: Giant-Size X-Men #1 -> May 1, 1975
2. Veronica Lodge from Archie Comics: 5,160
First Appearance: Archie Comics #1 -> January 1, 1942
3. Betty Cooper from Archie Comics: 5,154
First Appearance: Pep Comics #22 -> December 22, 1941
4. Wonder Woman from DC Comics: 4,206
First Appearance: All-Star Comics #8 -> December 1, 1941
5. Invisible Woman from Marvel Comics: 4,156
First Appearance: Fantastic Four #1 -> November 1, 1961
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