Opposite of Prompt?

[lwrath]

I would also like to do this even inside of a loop, just make it wait till I tell it to continue.

[Nyro]

It's not possible just like that.

While Maya is running/evaluating your script, particularly the for-loop, it sets its state to "busy". That means it never enters its idle state, which is necessary for you to be able to interact with it.

A possible solution would be to separate your job into 2 procedures:

the first procedure runs the for-loop until some condition is met, upon which it breaks the loop and stores whatever necessary values it needs later on in a global variable. Or you could create a scriptJob to take up where the first procedure left off.
In either case you need a second procedure that can be called when you are "done doing your work in Maya" that retreives the values previously stored and continues doing something with them.

[DeadlyNightshade]

Not possible afaik - there is no MEL "stop"-command.