Below is our compilation of funding opportunities for women in science. To suggest an addition, contact firstname.lastname@example.org 
American Association of University Women (AAUW) - Educational Foundation
AAUW offers several opportunities, including dissertation fellowships, postdoctoral research leave fellowships, selected professions fellowships, international fellowships, and career development grants.
Association for Women in Science Education - Undergraduate and Graduate Educational Awards
These $1,000 scholarships support both undergraduate and graduate education and include one set-aside award for a student who has interrupted their education to raise a family.
Daphne Jackson Fellowship
Daphne Jackson Fellowships enable women and men scientists and engineers to return to appropriate careers in UK universities or labs following a career break due to family commitments. A typical fellowship lasts two years and is held on a flexible part-time basis to enable the Fellow to meet ongoing family commitments.
Delta Gamma Women in Science Grants
The Delta Gamma Foundation offers scholarships for undergraduate work, fellowships for graduate study, and loans for any form of higher education beyond the sophomore year. Women in Science Grants, awarded on an individual basis, encourage Delta Gammas to pursue careers in science.
Maria Mitchell Women in Science Award
This annual $10,000 award recognizes an individual, program, or organization in the U.S. that encourages the advancement of girls and women in the natural and physical sciences, mathematics, engineering, computer science, and technology.
National Institutes of Health - Reentry Programs
NIH has two programs open to both men and women looking to reestablish a research career after taking time off to attend to family matters:
Mentored Career Development Award (K01) grants.nih.gov/grants/guide/pa-files/PA-00-019.html  Supplements to Promote Reentry into Biomedical and Behavioral Research Careers - grants.nih.gov/grants/guide/pa-files/PA-99-106.html 
Postdocs can apply for up to 4 years of mentored support.
Mentors with existing grants from the NIH can apply for these grants to support a person looking to reenter research.
Mentored Career Development Award (K01)
Supplements to Promote Reentry into Biomedical and Behavioral Research Careers -
National Science Foundation
The Professional Opportunities for Women in Research and Education program is no longer active. Look for the announcement in the fall of a new program--dubbed ADVANCE--that will look for institutional solutions to address the challenges faced by women faculty.
Natural Science and Engineering Research Council of Canada (NSERC) University Faculty Awards program
Canada's government science and engineering funding agency created the University Faculty Awards (UFA) program in 1998 to encourage Canadian universities to appoint promising women and aboriginal researchers to tenure-track or tenured positions in the natural sciences and engineering (NSE). Read NSERC Program Officer Candice Robinson's description and defense of the program  published on Science's Next Wave.
Sigma Delta Epsilon - Graduate Women in Science Fellowships
Fellows receive between $2,000 and $3,000 for predoctoral or postdoctoral study. Graduate students can also apply for $500 travel fellowships. There are no restrictions on nationality or place of study. Must be a member, but women can join Sigma Delta Epsilon ($25) when they apply.
Sloan Foundation Pre-Tenure Leave Fellowships
Provides up to $20,000 in matching funds to regular faculty--untenured or tenure-track--at selected institutions in the fields of mathematics, science, engineering, or technology faced with urgent family responsibilities so that they can take a leave with salary or, after a leave, resume research.
UNESCO-L'Oréal Grants for Young Women Scientists
In January 2000, UNESCO and L'Oréal announced the first 10 recipients of this new award program geared to supporting female postdocs in the life sciences. The $10,000 scholarships are the result of a partnership between L'Oreal and UNESCO and are aimed at helping women under age 30 establish careers in research. Recipients were selected from 90 nominees put forward by the UNESCO National Commissions.
Wellcome Trust Research Career Re-entry Fellowships in Basic Biomedical Science
Postdoctoral scientists in the European Union who have decided to return to a research career after a break of normally at least two years can use these fellowships to help them recommence a research career.