The Colorado elections used paper ballots (complete with "hanging chads") and from what I could tell were run pretty fair and square. One year there were some problems with some of the kids from the local college where rich Easterners send their lower-caliber offspring when they can't get into the Ivy League. They flooded a particular precinct insisting that they be given provisional ballots (name not on the list and ballots not counted unless it's close). They didn't meet the requirements even for those ballots and some threw a hissy fit. The local prosecutor discovered that many had already voted absentee back in their home state. They were not prosecuted, unfortunately.
In North Carolina in '06, the precinct captain ran it by the books. In '08, same precinct, same captain, many were allowed to vote provisionally even though they didn't meet the requirements (didn't live in the county they were trying to vote in). Others told me it was similar in other precincts.
Paper ballots, ID, and lots of well-trained observers seem to be the best way to avoid the threats from social engineering and hack attacks on the integrity of the voting process. I would even go for the purple dye they use on the thumbs of voters in some countries to prevent people from traveling precinct to precinct to vote for dead people and people who have moved away who are still on the rolls. (There are more than you probably think.)
In general, my observation has been that the voting process has become more corrupt over the past 20 years. It's just damn hard to catch it if the people who are supposed to enforce the rules don't care to.