My problem is that once the guest machine goes to sleep, I can't seem to wake it via Synergy. Is this expected behavior? I have WoL enabled, so theoretically I should be able to just move my mouse over to the sleeping monitor to wake it up.
You'd need to patch the synergy server to send a WoL magic packet[1] to wake up the client whenever it sends a message that might hit a client that's asleep. (some systems might support something other than the standard magic packet, but I don't know of anything else that works consistently cross platform.) Might also need to look at making sure the client connection comes back up clean and have some delay to make sure it's ready to receive whatever message started the process, and doesn't timeout while waking up.
I wouldn't have anticipated it, but this is an critical feature for me. Without WoL, I need to have a mouse/keyboard attached to the guest machine, which completely defeats the purpose of using Synergy.