The 4.6l is a pretty tough engine. You'll hear about issues with head gaskets on late '90's applications, valve seals on early 90's car applications, and intake manifold issues on some car based applications (trucks use a different manifold).
Look at it this way, its been around since the early 90's, and powers the Crown Vic which sees a boatload of fleet/police/taxi uses and does so pretty reliably!
The 4.6 in my '97 F150 ran like a top when I sold it with 163,000 miles. Last I heard its pushing 200,000, and the only thing ever touched on the engine has been spark plugs and wires (once!).
My '99 F150 has 114,000 on the odometer, and has the same story as the '97 - one set of plugs and wires, no other engine related problems.
Some get down on the 4.6l hp and torque numbers, but its always been up to every task I've thrown at my trucks, but I also am no stoplight racer!