BiggerPockets

I think more of strategies than tools, but here are the top two that come to mind:

1) Don't pay too much. Make sure there is enough margin in the deal for good profit, and then some more to cover whatever may go wrong.

2) Multiple exit options. If plan A fails, to be able to easily switch to plan B. For example on a rehab flip, say it doesn't sell for my target. Then it should also be the type of property that fits my rental criteria.

This tool has always worked for me:

http://www.youtube.com/watch?v=NUYKBIqGkoM

Seriously,
Use craigslist to find out what real rents are in an area (don't trust your realtor).

Demand closed comps (and ignore the list comps your realtor tries to sneak in)

Wikipedia your market to see what non-industrial amenities your market has to keep people there. (Universities, Bases of religious organizations, etc....)

Knowing your market can go a long ways to minimizing your risks. The numbers can be very good but if the market in the area is moving down and your trying to flip a deal your margin may disappear before the job is done.

Thanks for the responses everyone. It was helpful in our research on a product that we have created.