SpectorV, the car is an early 2000 (said in my original post), so it's one of the ones with the severe problem. There's nothing wrong with putting a breather on, so long as you can live with the smell (worse if you run the AC a lot).
00StangV6Coupe, PCV = Positive Crankcase Ventilation.
Basically, when your engine is spinning, you get peaks of high and low pressure in the bottom end of your engine. This is bad - if the pistons are having to fight positive pressure in the bottom end, it robs you of power. The answer is just to open up the bottom end (ie, don't seal it air-tight) so that the pressure doesn't build up. The hole on your valve cover is to vent the bottom end of the engine. Engines have had ventilated crankcases for almost all of history, but up until the 60s/70s, they'd always just be vented into the air with a breather cap.
Since the emissions laws got tighter, you can't vent that into the air any more. There's all kinds of nasty oil fumes and spent crap floating around in there. Very bad for pollution. So for the last 3 decades, the government has required that those fumes not be allowed to escape into atmosphere, so manufacturers recycle them back into the intake. There it gets burned cleanly.
If you have a poorly designed PCV system (like my POS Mustang), or a bad PCV valve, it can suck oil into the intake. Passing all those nasty oil fumes into the chambers to be burned hurts power a bit (I must stress a BIT - might rob you of 0.5hp, really not worth worrying). You're fine removing the PCV system, just be aware that depending on your local rules, you may or may not pass emissions, and your conscience may have issues with venting all those bad fumes into the air.