var number = null;
while (number !== 0 && !number || number >= 100) {
number = parseInt(prompt('Enter a number, less than 100'));
}
document.write(
number +
' is less than 100 by ' +
(100 - number)
);
This puts us in a loop for whether or not the number is a valid integer (I assumed that's what you wanted, but you could change this to float or something else), and under 100. Only when the user's input is valid will it go to the line to output.
The second condition for the while loop is !number. This basically tests for falsy conditions, such as NaN or null. If parseInt() can't figure out what the user typed in for a number, it will return NaN. And, of course, we initialized the number variable to null.
The first condition for while is number !== 0 is actually required because of the second condition which tests for falsy. 0 is falsy, but 0 is a valid number less than 100, so we need to make sure that we let 0 be valid. Conditionals like these short circuit. That means that they are processed from left to right, and any condition failing the test will immediately bypass the conditional block of code below. If number is 0, we know that the whole condition is false and we can move on.
The third condition simply ensures we're under 100 by re-prompting if we're not.
Also, I should note that document.write() has some issues. It's better to select an element on the page and set its text.