I used to do this in my prompt, but it caused more problems than it solved, since sometimes programs actually put legitimate output on the last line without a terminator.
The simpler fix is just to notice that your prompt has shifted over (it's almost impossible not to notice) and just hit return before doing anything.
I added a newline (\n) to the beginning of my prompt. This way I never lose program output -- and also it's easier to see where previous commands begin and end in the scrollback buffer.
My prompt is five lines tall, including three blank lines. I did that, along with some bright green coloring, to make the prompt easier to spot as I rapidly scroll up through a mountain of output from my last command.
The simpler fix is just to notice that your prompt has shifted over (it's almost impossible not to notice) and just hit return before doing anything.