I always lock my laptop when I'm not using it, and I keep the lid up when I leave my house, but I find that someone almost always shuts the lid. This prevents me from connecting to my TLS-encrypted FTP server. I was wondering if I can instruct ProFTPD (or computer processes in general) to keep running when the lid is closed in Xubuntu 11.10. I read about Wake-on-LAN, but that seems to be for the local network at my house. Any suggestions?
You should tell your Ubuntu to stay awake (not going into stand by or hibernate).
Wake-On-LAN works with a magic Ethernet packet. As you cannot route the packages, it as you already know, only for the local network. But you can use another computer in the LAN (if there is any and alive) to wake your laptop.