USA Today (today) has a story about the Brennan Center report on vulnerabilities with electronic voting. I have not read the entire report–it is 162 pages–but it does address key issues with the security of voting technologies.
Given the work I am doing that is complimentary to this, examining the election laws and procedures that address all voting technologies and the counting of ballots, I can say that the key to addressing many of the problems discussed here is having detailed procedures in place to address the security vulnerabilities that are in the report. In many cases, the security problems can be rectified through effective training and procedural requirements for handling ballots and machines.
Likewise, Common Cause has a report on electronic voting vulnerabilities as well. I think that the key take away from this study is this–if you have VVPATs, audit them! It is silly to have the VVPATs and then not use them for auditing purposes.