Could CiviCRM 4.5 or 4.6 make it easier to generate large numbers of PDFs at once?
Are you using the wkhtmltopdf option in CiviCRM:

Administer CiviCRM >> System Settings >> Misc

http://d46.demo.civicrm.org/civicrm/admin/setting/misc?reset=1

Its a local binary installation (needs to be done by your system admin), but gives you a lot better performance than the php pdf libraries shipped with CiviCRM