Well, I have yet to start any mods on the 4.0L in my Explorer, but my former vehicle was a 94 Ranger with the 4.0L. The only mod I had on the engine was a K&N Filtercharger system, and I loved that... made throttle response quicker, and it revved easier. I was planning to put a Flowmaster 50 series muffler with 2.5" pipe, JBA headers, and a Superchip. These mods will get you plenty more HP, and if you really wanna get nutty, there are a few supercharger systems out there (Vortech, BBK, Paxton). A guy I know has a Vortech on his 97 4.0L Ranger (also has Pacesetter headers, Flowmaster exhaust, a few other goodies), and it absolutely hauls ass.
For my Exploder, I plan to simply upgrade the intake system, exhaust, and add a Superchip, just for some cheaper horsepower and to improve gas mileage a bit once I get the lift and larger tires.