OpaVote is a huge proponent of using better voting methods. The point of voting is to represent the will of the voters, but the most commonly used voting method (plurality voting) often doesn't do that well.
Especially with online voting, it so easy to implement better voting methods, such as instant runoff voting, single transferable vote, Condorcet, or approval voting. Many organizations support these kinds of voting reforms, and I'll keep an up to date list in this blog post. Let me know if I missed a good organization.