Package files make more work for a developer but much less for the user. As a result, they are the method of choice when a software package requires files be stored in more than one folder on the user's hard drive. They also allow the user to choose different types of installation, such as just an update, minimal installs, or developer installs.
When you make a Software Valet package, there are a few considerations to keep in mind. Installing shortcuts are a pain in the neck unless you have a fixed install location and you make separate packages for Zeta and R5. You should also make sure that all the little details, such as version, build date, and so forth have been set to the proper values. Lastly, test the installation before actually releasing the software to make sure that it actually works the way that it should.