Security guru Bruce Schneier examines Papal election security:
Probably the biggest risk is complacency. What might seem beautiful in its tradition and ritual during the first ballot could easily become cumbersome and annoying after the twentieth ballot, and there will be a temptation to cut corners to save time. If the Cardinals do that, the election process becomes more vulnerable.
A 1996 change in the process lets the cardinals go back and forth from the chapel to their dorm rooms, instead of being locked in the chapel the whole time, as was done previously. This makes the process slightly less secure but a lot more comfortable.
There are also enormous social -- religious, actually -- disincentives to hacking the vote. The election takes place in a chapel and at an altar. The cardinals swear an oath as they are casting their ballot -- further discouragement. The chalice and paten are the implements used to celebrate the Eucharist, the holiest act of the Catholic Church. And the scrutineers are explicitly exhorted not to form any sort of cabal or make any plans to sway the election, under pain of excommunication.
Of course, no amount of security in the world will prevent the electors from replacing Joseph Ratzinger with someone at least as out-of-touch and reactionary as he is, given the constitution of the cardinality these days.