Hundreds of manuscripts of the New Testament exist, and they differ among themselves in literally thousands of ways. The text that is printed in modern Greek editions of the New Testament (and which is translated into other languages for use in homes, schools, and churches) is a composite, made up of readings drawn from all these different documents. Scholars laboriously compare each extant copy, word by word, and choose which of their varying readings is the most ancient and authentic.
Though the overall quality of some manuscripts is better than others, no single manuscript is perfect in every detail. Many are damaged or missing pages; others, though quite good overall, are occasionally marred by scribal errors. No "original copy" exists; in fact, there are no New Testament documents from the first century at all. Even those from the second century are quite scarce and always incomplete.
Study Bibles will occasionally have footnotes that point out important variants. For example, the New Revised Standard Version of Revelation 13:18 reads as follows:
This calls for wisdom: let anyone with understanding calculate the number of the beast, for it is the number of a person. Its number is six hundred sixty-six.1
If you follow that footnote, you will see the following statement: "Other ancient authorities read six hundred sixteen." Either the largest number of manuscripts, or the manuscripts of the best quality (in this case it happens to be both), prefer the 666 reading, which is why that number is placed into the text of your Bible. However, a few manuscripts put a different number into this verse, and the variation is flagged in a footnote.
Each variation is called a reading, while each manuscript that uses a particular variation is called a witness. One might ask, "How many witnesses does the 616 reading have, and how dependable are they?" The dependability of a witness depends on a lot of factors: the age of the manuscript, the skill of the scribe who wrote it, the number of errors it contains, and so on. Like all scientists, scholars of the New Testament move from the known to the unknown: if a manuscript garbles numerous passages that we have confidently reconstructed from dozens of other witnesses, then other uncertain readings are probably garbled in this manuscript as well. (Probably.)
In a study Bible, important variations are marked in this way -- changes in meaning or sense that might have relevance for the average reader. However, in a complete apparatus criticus, every single change is footnoted across all relevant manuscripts. This includes, not just changes in meaning, but also changes in verb tense, the spellings of proper names, switches between nouns and pronouns, shifts in word order, and so on. These details may feel irrelevant to a small-town pastor preparing the next morning's sermon, but they have tremendous relevance for scholars, because minor changes in spelling or phrasing can help date and locate manuscript traditions. (If, for example, an unusual spelling occurs in only two manuscripts, it is possible that those two manuscripts came from the same century or the same part of the world.) Of course, variations that do change the meaning of a text are even more interesting, since they might teach us about the type of Christian belief or practice that was popular in a certain time or place.
Needless to say, the apparatus for the New Testament is immense. It takes up a much larger proportion of each printed page than the actual text does. To make the list of variants easier to navigate, scholars of the New Testament have developed a series of short forms, called sigla (singular siglum), that represent the most important or commonly-used manuscripts.
For a picture of a page out of a modern New Testament with apparatus, see
this site. Note that the entire visible section beneath the dividing line contains the notes for a single verse of the gospel.
The advent of computers has made the use of apparatus much easier than it was a hundred years ago. The Stuttgart Electronic Study Bible, or SESB, is a very useful (but expensive) apparatus for Microsoft Windows.
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