Does anyone know of an automated way to enable Wake on LAN capabilities in the BIOS?
There is a linux tool called nvram-wakeup that allows you to programattically set the wakeup time of a box - but I think it also allows you to manipulate other bios settings.
smbios-utils is another utility worth looking at.
You could also check out the forums for MythTV, as that's where I first heard about this. I know they deal with setting up wake-on-lan configurations - but I have not done that myself.
Check to see if your motherboard manufacturer provides cmos/bios backup utilities (usually used just before upgrading the bios). If so, you can likely get one machine set up the way you want it (including Wake-on-Lan), save those settings, and then restore them on other (identical) machines.
If your motherboard manufacturer doesn't provide such utils, perhaps Flashrom will work.