PowerCLI is a CLI based on Windows PowerShell and leveraging the vSphere SDK for .NET and runs only on windows as a remote CLI - http://www.vmware.com/support/developer/PowerCLI/index.html
vCLI is a CLI based on vSphere SDK for Perl, and since it's Perl, it can run on Windows, Linux or MacOSX
They both have support for remote management of your vSphere infrastructure from host management/configuration to other operations such as managing vCenter, VM, etc. Depending on the platform you use for management, you'll want to use one or the other. All capabilities are available in both CLIs, but you may need to write some custom scripts with vCLI if a certain capability is not available out of the box.
Good place to start if you're new to vSphere 5 is the documentation center - http://www.vmware.com/support/pubs/vsphere-esxi-vcenter-server-pubs.html