In the previous article Making Electronic Voting Transparent, I proposed an electronic voting system that allowed the voter to check how his or her vote is recorded in the official vote database. In that system, the voting machine printed a hardcopy receipt for the voter to take home. The receipt showed the vote record and had a serial number that the voter could use to later check the database of votes cast which would be made available online. Nobody but the voter would know the serial number for her or his vote.
Here is how such a system could cheat. The system could memorize the ballots cast, so that it could give all the voters who voted exactly alike the same serial number to check. The actual vote on all but one of these ballots could be modified fraudulently, but the fraudulent votes would have serial numbers that are never printed out for any voter.
If the voting computer program source code were viewable by the public (this is called open source), then experts could look at the code for assigning serial numbers to make sure nothing like this was built in to the software. So, my proposed system could be kept clean of such attempts at fraud.
You also may want to look at a previous post Standardize Electronic Voting Technology. There is already a government agency that could oversee the creation of a standard for electronic voting systems.