THe 5.0 is the old Windsor engine that's been around since 1962 in various displacements. It's your typical pushrod engine with an in-block cam. The 4.6 is a relatively new engine that was the first of Ford's Modular V8 family. It's an overhead cam design, meaning no lifters or pushrods. The 5.0 has a huge aftermarket following, since it's been the engine of choice in Mustangs and other performance Fords since way back, and the 4.6 is getting there now that the SN-95 Mustangs are gaining legitimacy in racing.
If I had my druthers, I'd go for the 5.0 over a 4.6. We had a 99 GT with the 4.6, and although it's a great engine, aftermarket parts were about twice the price as for comparable 5.0 Mustang parts. Plus I don't like the new Explorers they put the 4.6 in. On the other hand, if you can get past the new styling, the 4.6 probably gets better mileage, and has a higher hp rating from the factory. Hope this helps.