I run a fair number of batch processes, and will generally turn my attention to a second monitor/activity while I wait for it to finish. I'd to setup the terminal (For what it's worth mentioning: Putty terminal SSH'd to server) so that the terminal will flash a color to get my attention. I know there is a beep command you can use, but it won't work in this case.
So, in my mind I see this being two parts- both useful separately: (probably...)
- Have a watcher process that detects when a single command has been running a while
- Set background color to flash once or twice once watcher process is triggered.
I have no idea if this is within the realm of possibility, but thought somebody might!