Did you even bother to check the file properties? On my WS 9.0.0 install, while the file sizes are slightly different nonetheless, they are the same version. Regardless of version, generally speaking, they do the same thing... so you can use either.
The reason for there being two is that the VMware Workstation and VMware VIX are separate packages, even thought VMware VIX is being installed with VMware Workstation 9.x it is also available as a totally separate download.