Do you have a cdrom/dvd listed in your sources?
If so comment it out or upgrade to APT 0.8.9:
* cmdline/acqprogress.cc:
- don't ask the user for media change if quiet >= 2, stdout is not
a tty and assume-yes, force-yes or trivial-only option is set to
avoid cpu eating endless loops in unattended runs like apt.cron
(Closes: #602354, LP: #665580)
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cron.daily/apt script hung
https://bugs.launchpad.net/bugs/683277
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