As far as I know - you would not want to pass through hardware that needs to be used by multiple VMs, as once the hardware is passed through to a single VM, it is no longer available for use for the other VMs.
As far as passing through a USB controller vs. just assigning a USB port during run-time -- I think it is a decision that can be based on whether or not you consider the passed through USB something that you want permanently assigned, or not. After a VM or host reboot, for example, items that are passed through will just re-appear on the VM, and not need to be manually re-associated with the VM.
In my use case, for a test ESXi server, I have a RAID controller passed through to a Linux VM. That VM is a NAS that serves drives via NFS and SMB to both other VMs and other physical machines on my network. I also have a graphics card, and USB controller with keyboard and mouse that I pass through to a Windows VM. This allows that VM to be used like a "physical" PC, including higher performance video output that often does not work so well on a "straight" VM.
Just my use case -- might be able to help you determine when to use passthrough devices.
John
