We've also used pdftotext (see Sklivvz's answer) to generate ASCII versions of PDFs and wdiff to compare them.
Use pdftotext's -layout switch to enhance readability and get some idea of changes in the layout.
To get nice colored output from wdiff, use this wrapper script:
#!/bin/sh
RED=$'\e'"[1;31m"
GREEN=$'\e'"[1;32m"
RESET=$'\e'"[0m"
wdiff -w$RED -x$RESET -y$GREEN -z$RESET -n $1 $2
