With the Papal Election only four days away, Bruce Schneier has taken a look at the process from a security standpoint. I found this to be quite an interesting read, since virtually all the information I have about electing a new Pope came from reading Angels & Demons. It seems that thousands of years of tradition have refined the system down to a rather secure process.
While reading the article though, a few weaknesses did stick out at me. Bruce mentions most of them, such as the first Scrutineer being able to replace ballots with a substitute one, the fact that there are extra ballots floating around the Sistine Chapel, or that the Infirmarii have a the ability to forge a ballot if they really wanted to. However since the Infirmarii, Scrutineers, and Revisers are randomly selected for each vote, the odds of being able to abuse one of those positions in order to change the outcome are pretty small. Additionally, since everything but the actual writing of a name onto the ballots themselves is done so that all the cardinals can watch, it would be very difficult for someone chosen for one of those positions to modify the election results.
The one thing that really stuck out to me was that before the voting begins, "trustworthy individuals of proven technical ability" help the cardinals to detect eavesdropping devices. This is the one point where someone who is not a cardinal is allowed to participate in the voting process, and it seems to me one of the easier ways for an outsider to affect the outcome.
Updated 5:38PM to reflect the correct Dan Brown book :-)