Used, Pre-Certified have been thoroughly inspected. The major vehicle system of each Pre-Certified car (e.g. brakes, engine, drivetrain, steering, suspension, tires, wheels, exhaust system, vehicle interior, and vehicle exterior) are in "like new" condition.
I have a Used, Pre-Certified Honda Civic. It's a 2005 that I purchased in 2008. IIRC, there was 35,000 miles on the car. It came with a warranty for up to 50,000. I opted to extend the warranty to 100,000. I actually used the warranty - several times - so I am glad I did.
I will say that I had to work to find a Used, Pre-Certified Honda Civic. There weren't that many for sale, and the Pre-Certified Hondas kept getting snatched up.
I will also say that a used Honda, especially a Pre-Certified one, is not that cheap. There was a brand new SUV - it was either a CRV or an element - that was cheaper than the Pre-Certified civic I purchased.
Also about used/pre-owned cars right now - this is not a good time to buy a used car in the US. The cars that were flooded by hurricane Sandy have been cleaned up and are now hitting the used car market. It is not possible to restore a flooded car. Those cars will always be unsafe.
If there's any way you can afford a new car you should get a new car. Or keep driving your old car for a couple more years. Do not buy a car that has been flooded.
Having a Used Pre-Certified vehicle should get you around this. The Pre-Certifieds are inspected and "brought up to snuff" by the dealership, which sells them with a warranty. It would not be cost-effective for a dealership to take a flooded vehicle and pre-certify it.