I have both and have used both! Aptbackup has always worked for me. It's simple, no options other than backup or restore, and it's quick. It just doesn't backup your springboard layout, like icon order and some themes. It'll remember your current springboard theme, but will not remember which ringtones ToneFx had assign.
Pkgbackup is cool. Has many more features, and even more with OS4. It can backup to the phone or to an online dropbox account that you have to create. In combination with SBOrganizer, it can back up and restore your springboard layout. It also does autoback up reminders, backs up upon opening the app, and allows a back up schedule to be set. It also tells you exactly how many apps are installed and how many are backed up. But the price is now $7.99!
Honestly, if you really don't want to spend the money, Aptbackup is just fine!