Another method that I sometimes prefer is to use the presentation software of your choice (e.g. PowerPoint) and hyperlink the notebooks into that. For some things like showing lots of images (especially fullscreen) Mathematica is not very handy (yet).
You can simplify the preparation for this by opening and evaluating all these notebooks up front. For some presentations that use a lot of different slide-containing notebooks I put all those in a subdirectory ("./Mathematica/") and use an organisation notebook containing the following code:
files = FileNames["*.nb",
NotebookDirectory[] <> "\\Mathematica\\"][[1 ;; -1]]
nbs = (UsingFrontEnd[nb = NotebookOpen[#];
SelectionMove[nb, All, Notebook];
FrontEndTokenExecute[nb, "EvaluateCells"];
SetOptions[
nb, {WindowSize -> {Full, Full}, WindowToolbars -> {}}];
SetOptions[nb, ScreenStyleEnvironment -> "SlideShow"];
FrontEndToken[FrontEnd`SelectedNotebook[], "ScrollPageLast"];
nb]) & /@ files;
SetSelectedNotebook[EvaluationNotebook[]];
Button["Last Slide", (SetSelectedNotebook[#];
FrontEndExecute[{FrontEndToken[FrontEnd`SelectedNotebook[],
"ScrollPageLast"]}]; #) & /@ nbs]
FileNames["*.ppt*", NotebookDirectory[]][[-1]] // SystemOpen
Button["Close all notebooks", NotebookClose[#] & /@ nbs]
This opens and evaluates all the notebooks in the subdirectory and sets them to FullScreen and SlideShow mode. Finally it opens the (last) ppt in the current directory and provides a button for going to the last slide of each notebook and closing all opened notebooks.
With this setup, you can simply call up the notebooks via Hyperlink and Alt-Tab (on Windows) back to the running presentation.
Of course, I´d rather use Mathematica only, but for some of my presentations this works all right for the time being. If you keep to the same directory structure, the code can be reused pretty well.