Paper and pencil aren't a perfect solution either. This page shows a few examples of where things have gone wrong.

http://blogs.mprnews.org/newscut/2008/12/timewasters_the_bal...

In the case of the Florida Presidential vote, they ran into the problem of "hanging chads" where parts of the page that were intended to be fully punched-out so a machine could detect the vote were still attached to the page, leading to further scrutiny over deciphering the true intent of the voter's ballot.