Is there a way to programmatically reach into the BIOS and turn on the Wake on LAN capability for those machines that support it?
Ideally, the solution would be cross-BIOS, but hitting each of the major vendors with separate solutions would be okay, too.
BIOS configuration is something that the OS intentionally limits to avoid virus problems (lots of bios viruses back in the day!).
You need to look at the system management interface to see if it's available generally. You'll probably need to work in ring0 in windows (or root/kernel in linux). Additionally, you'll likely need to learn how to do this accessing the hardware directly, learning and keeping a database of the most common BIOS manufacturers and types, and even then won't be able to cover all of them.
SMBIOS might help?
I know we had a utility to read the BIOS from a regular windoze program once, at my previous job.
@TALlama: Did you find a solution? I'm in the situation as you, want to programmatically enable Wake-On LAN in bios.
I think you're going to find that Wake on LAN is a CMOS Setup option, and so not programmable via hardware-agnostic OS interfaces.
Dell Inc. provides customers the OpenManage suite of utilities for remotely manipulating Setup settings on its client machines. Some links: