Unashamed plug from me for some of the organisations I'm involved/have been involved with:
The Halo Trust - www.halotrust.org/home/index.aspx
I know its not a women's charity, per se, but women are hugely affected as the foragers, water carriers and wood collectors in many countries by the issue of landmines. In particular, the work they are doing in Jaffna (Sri Lanka) is inspirational.
The UN Refugee Agency - www.unhcr.org/cgi-bin/texis/vtx/home
I'm working on a project with them on the Thai-Burmese border aiding refugees, mainly women and children, from one of the most silenced and oppressed countries in the world
After the Wave -
www.afterthewave.org/
Local organisation helping tsunami-affected children in Thailand
Whole Planet Foundation -
www.wholeplanetfoundation.org/
Fabulous micro-credit organisation, which, alongside awesome commercial ventures such as the Grameen Bank www.grameen-info.org/ are transforming the lives of the rural poor, including women. I heart micro-credit - I've seen first hand the immense difference it can make in small communities and families.
The PDA "Cabbages and Condoms" projects. Cabbages and Condoms is a Bangkok restaurant which is non-profit making, donating profits to the PDA projects on HIV/AIDS in Thailand. Including many projects helping women affected by HIV/AIDS. Also serves amazing food - if you are ever in Bangkok, go along and enjoy an amazing meal which directly benefits those in need - a win win! Apart from that, the PDA works in micro-credit, family planning etc:
www.cabbagesandcondoms.com/project.php
Friends of Bangladesh - a really small charity which fundraises largely amongst the British Bangladeshi community to support some excellent projects in Bangladesh, providing education and training for disadvantaged women and girls. I've visited some of their projects in the last few months - inspirational:
friendsofbangladesh.com/
I have a few more as well, but might save them for later!