Yes, Spybot-S&D has full support for PE in general and PEBuilder. You can download the necessary plugin for version 1.4 here (online link) or for version 1.5 here (online link), or run it from your harddisk after booting a PE disk.

Once run from your bootable PE CD, Spybot-S&D will automatically scan all registry and drives it can find (if you want that feature without PE, see this FAQ entry.