Now this depends on how the software was packaged, whether or not it supports scripting or transform files, etc.
In some cases (i.e. Microsoft Office), you can do a complete or total install. This will typically install all options at the beginning instead of upon first use. If the software supports this, in most cases it will also support a transform file (MST) to allow for this and other options to be scripted in.
Ultimately, it depends on how thorough (or lazy) the original programmer was when they wrote the installation package.
And I agree with George, if you can utilize SVS layers, it can make software distribution / maintenance a whole lot easier. A word of caution though... TEST TEST TEST. If you go this route, test it multiple times and include others in your testing. What works great for you, may not work so great for an end user whom uses it a lot different than you do.
I can't speak much for NS software deployment. That is the next thing on my list of items to do when I have some time.