Jesus taught "For where your treasure is, there will your heart be also.". This shows us that the key to any pro-life progress is in how much it costs us. "Follow the money" is good advice, and not just in a worldly sense. Specifically, pro-life people ought not be paying for abortions. How can we pray for life and then pay for death? For this reason, I rate Life Decisions International (LDI) near the top for their pro-life efforts. Briefly, these folks are leading the boycott of abortion-friendly corporations, and have succeeded in 'converting' over 100 corporations to an abortion-neutral corporate policy. This is a significant blow to the abortion juggernaut, and an essential part of the battle. More importantly, it is a way to purify our other pro-life prayers and labors. (It is this idea which eventually inspired the next step, that of resisting the tax-funding of abortion. Same principle: why pray for life and pay for death? See the Pro-Life Strike site for more on this.)
The most crucial pro-life battles are in other parts of the world. For this reason, I nominate two groups that focus on the international scene. Human Life International (HLI) is the only pro-life presence in many countries, and are single-handedly, with God's grace, challenging and holding back the forces of death in these locations.
In the same vein is The Catholic Family & Human Rights Institute (C-FAM), who do yeoman's work in pro-life advocacy at the United Nations. Two posts below   tell just a little of their vital efforts in defending human life around the world, and the real impact they are having.
Rounding out my list of personally vetted charities are two Chicago-based organizations with whom I have had personal involvement. They are Miles Jesu, a lay religious order, and The Women's Centers, with its series of free clinics. And my friend in Canada, David Little, whose unique mission has been the subject of earlier posts. See this article for the most recent development.