So on a topic that is not by any means new, however one in which I have been getting a lot of recurring discussions around lately from my customers...

So there seems to be a lot of different viewpoints on when or whether to re-package software for the purposes of automatic distribution (using ConfigMgr of course!).  For years, I have employed the following guidelines - in this order:

1.  Does the software natively support MSI?  If yes, no need to re-package, use the built-in characteristics of MSI to create a silent install command line (with or without transforms) to get the job done.  If not, consider Step 2.

2.  Does the software support any documented way to deploy the software silently?  If yes, great, use what the vendor gives you to get the job done.  If not, or it is not very clear, consider Step 3.

3.  Conduct research on sites such as www.appdeploy.com (one of my favorites, btw) to see if someone in the community has posted steps/tips on your software that allows for silent and automated deployment.  If so, employ these in the lab to confirm they work and then deploy.  If not, consider Step 4.

4.  Utilize your favorite MSI re-packager.  ConfigMgr users can use Macrovision's AdminStudio:  Configuration Manager Edition to get the job done.  But if you have purchased the Wise Installer and like their interface better, go nuts! 

As a rule, I always attempt to go down the past of least resistance yet maximizing supportability.  I see Step 4 as the worse case and most expensive as it is the most time consuming and you run the risk of the vendor no supporting your deployment if they do not support the re-packaging of their application.  IMHO, if the app is not native MSI but has a documented way of silently deploying, I say use it - supportability to speed far outweigh some of the ability built into an MSI wrapper...

Anyway, that's my $.02 - I will stop rambling now...