Merging Objects

There are 2 terms and processes.

1. Merge or Combine, where 2 or more objects are combined and treated as one, even though they still remain individual components (usually referred to as solids, bodies or shells). 

This merging process is what Repetier does.  You can open up multiple STLs, even intersect them and then save the platter as a single STL.  But if you were to open it in a program like NetFabb, or MeshMixer, you can separate the objects/shells again.

2.  Boolean is an operation where two or more objects that intercsect each other can be either added to each other, subtract one from another or create an object only from the parts that intersect.  The result of a Boolean operation is a single object or shell.

Boolean operations are much more complicated and sometimes take a lot of time to execute, and they may even fail if the algorithm cannot find the correct solution.

For the purpose of 3D printing, a Boolean'ed, single shell object, is desirable, as it will not have any intersecting surfaces that could create errors. 

However, most 3D slicer's have the means to deal with some of the simpler errors like intersecting planes.  However once in a while you find that a part of an object did not print, even though it's clearly visible, and that is usually due to some type of error that the slicer could not resolve (inverted surfaces for example).

Edit:
Here is a cross-section illustration of a combined object (sphere and square beam), and a Boolean add version of the same.