Maybe with some clever use of zsh hooks? Here's a gist for zbell; it uses `preexec` and `precmd` to run something right before a command is executed (`preexec`) and right before the prompt is shown again (`precmd`)

https://gist.github.com/jpouellet/5278239

Mine blinks a little light if a command finishes after 30 seconds, and sends me an email if something takes over a minute.