Like craft said, you need to think in EV/EBIT or EV/EBITDA. By using either of those ratios you get an idea of the unlevered cash flows of the business v the amount of capital (debt and equity) used to fund the business. If the unlevered cash flow of two assets is identical and the assets themselves are identical, then you'd pay the same price to buy either of those assets.
Hmm. I will look more into it. I have avoided this issue by simply looking for companies that do not have much debt.