Obviously figuring out TCO when you look for desktop alternatives is important. I did a quick search on what is out there. Check these out:
1. RedHat TCO calculator: considers savings from not renewing/signing Microsoft Enterprise Agreements, Moving from Windows to Linux desktops, servers, etc.
2. Omni has a Novell desktop TCO calculator: http://www.omni-ts.com/linux-desktop/tco-calculator.html
3. Virtualization (including desktop, but looks like windows based) TCO calculator: http://www.alinean.com/P_TCOcalculator.asp
4. Small Business solutions: http://www.bilal.ca/how-to-save-money-with-lotus-foundations/
5. ROI around Messaging and collaboration: http://www.permessa.com/roi_calculator