Yes, Spybot-S&D has full support for PE in general and PEBuilder. You can download the necessary plugin here (version 1.4) or here (version 1.5), 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).