Shawn,
In angling terms (especially here in PA), the distinction is often a loose one. Some PA streams are easy to classify as one or the other, and some have both characters within their watershed or within the course of the stream. Here in PA, limestone underlies much of what is known as the Great Valley, a long valley that curves southward alongside the Kittatinny Ridge. (The Cumberland Valley is in the southern part of the Great Valley in PA.) Belts of limestone or marble also exist in a number of other locations around the state.
Typically, PA freestones originate on mountainsides and are feed by seeps and hardrock springs. They tend to be more acidic and the hardrock base offers little buffering capacity, making them much more vulnerable to acid rain. They often have waterfalls and extensive pocketwater in areas with a steep drop, or a classic pool-and-riffle configuration. Because of low alkalinity, they are less fertile than the limestoners, but can have a greater variety of aquatic inverts (when healthy).
PA limestone streams might be loosely grouped into three categories: limestone spring creeks, freestone streams that are significantly influenced by limestone tributaries, and freestone streams that flow over a limestone base for part of their length. Of these, limestone spring creeks are the exemplars, and some of these emerge full-blown from high-volume springs that issue from limestone caverns. These caverns or sinkholes can also appear in the course of the stream, causing some to go underground at points along their course.
Classic limestone spring creeks, like the Letort, derive most of their volume from the headwater springs, often have a flat meadow character, host abundant weed growth, and have a more consistent temperature than freestones. Other true limestone spring creeks may have similar origins, but develop an atypical character due to terrain or the influence of non-limestone tribs. Penn's Creek has classic limestone origins, but picks up freestone and limestone tribs along its course and flows through varied terrain, giving it a diverse appearance and very diverse population of inverts. Big Fishing Creek is similarly diverse in terrain and critters. Spring Creek is more classic and has a less diverse assortment of water types and critters. (Some of the lack of critter diversity is also due to pollution, but even in perfect health, it still would not display the diversity of Penn's and Fishing.)
Some of the other streams we call "limestoners" here in PA come by the name through less direct means. These streams are basically freestone in origin, but are changed by the influence of significant limestone feeders or by flowing for some distance over exposed limestone belts. Such streams fit into the limestone category by degrees, and depending upon where you are on the stream, they may or may not display a limestone character.