Of course, some applications are installed without the use of package files. These apps often do not require support files, or they create them at first launch. As such, they can be installed simply by copying them to a Mac's Applications folder or the Applications folder inside a user's home directory to limit access to just that user.
Other applications, most notably software from Adobe, may use a proprietary installer. For these cases, you can use package file tools to take snapshots before and after installation to create an appropriate package file for the application, if needed. You can also include such files in a monolithic image or use a deployment tool that supports the proprietary format.
Note that package files can simply include files and no actual applications. This makes them an ideal way to mass deploy updated configuration files or documents to specific file system locations.
Apple's deployment and patch management tools
Apple provides a number of deployment and installation tools. These include Disk Utility for creating system images and Apple Software Restore for deploying images locally or using a unicast or multicast network connection. Package Maker, available as part of Apple's developer tools, can be used to build package files and code the installer command to install package files in the background, even via SSH. All of these features are available free of charge. (For an overview of these and other mostly free Mac management tools, see "22 essential Mac tools for IT admins.")
As far as commercial tools available from Apple, OS X Server's NetBoot, NetInstall, and NetRestore can be used to streamline monolithic image deployment, enabling you to set up a network-based deployment operation for installing a variety of specific package files. This option allows you to combine a small number of base images with specific packages to automatically customize your Mac fleet during deployment. NetInstall can even be configured to roll out nonsystem package collections.
OS X Server also includes a Software Update Server feature that mirrors the contents of Apple's update servers. This offers two advantages. First, by mirroring updates locally, it improves update performance while reducing the load on your organization's Internet connectivity. Second, it allows administrators to vet updates for problems before making them available. It does not, however, provide a mechanism for ensuring updates are distributed, and it cannot be used to provide non-Apple updates.
As mentioned above, the scalability of OS X Server functions has become limited due to Apple's decision to stop producing enterprise-grade server hardware. For mass deployments using only Apple technology, the ideal solution is Apple Software Restore running in a multicast configuration -- with Apple's NetRestore to automate deployment completely or a series of bootable drives (even small flash drives) with a technician touching each machine to initiate the deployment process.
Finally, there's Apple Remote Desktop, which can be used to remotely deploy package files, run scripts, and perform other user support and administrative functions, including hardware and software inventory, to ease license management. Apple Remote Desktop is the Swiss Army knife of Mac management, an invaluable tool that every organization should consider purchasing even when supportly just a handful of Macs.