If you're already using microcontrollers, why not emulate a USB keyboard with one, and have an IR sensor that triggers a key press when it gets a signal?
One thing I just thought to try is using an app on my phone to send the WOL packet.
Edit - the other thing that came to mind was to look into HDMI cec and see if there's a setup where turning on your tv will turn on the PC automatically.
Edit 2 - if you go with an app, you could use something like tasker and then you can have different triggers like your phone tapping an nfc sticker (then you don't have to unlock and find an app).