Application repackaging is seen by many as unnecessary, and certainly in small, simple environments it may not be required.  If all the software you use is common, off the shelf software packaged in Windows Installer format, it indeed may not be required.  In more complex environments, especially those using an automated application deployment methodology, repackaging of many applications is necessary.

Ideally applications should be repackaged into Windows Installer format(MSI).  MSI is the only packaging that Microsoft allows under the "Made for Windows" certification program.  There are currently no other insaller systems that track shared components & is as widespread as MSI.  While there are other systems that attempt to track shared components, without the widespread adoption of those systems they are not effective.

Whatever packaging system you adopt, all the applications deployed should be in this format.  This naturally makes MSI an ideal choice since many applications you purchase will already will be in this format and you will only need to either create and apply a transform to provide the customizations to the package you require, or in many cases command line properties during the install sequence will be sufficient.

Repackaging software is essential for this process.  You can see a large range of packaging software on http://appdeploy.com .  My personal preference is Wise Package Studio .  In my opinion Package Studio offers functionality other systems have not yet quite achieved.  It is certainly the rolls royce of repackagers, at a price similar to competing products.  Some argue it is overly complex, but while it is not for beginners it gives the repackager complete control over the installation.

I can offer complete repackaging services & have experience repackaging extremely complex applications.  Please contact me for more information.