One thing to consider - CS6 is only 64bit (on the Mac at least). Plug-ins that are 32bit only will not run in the 64bit environment. Also, if you install CS6 over CS5, everything should be fine; however, if you subsequently choose to uninstall CS5, make sure you use the uninstaller so you avoid removing files that may be common somehow. If you uninstall CS5, make sure you deactivate it before you uninstall.
The plug-in structure for CS6 is slightly different than CS5, so read up on your specific plug-ins to see how they may be affected. I would recommend keeping CS5 around until all of your workflow applications are running in CS6 without problems (i.e., 32bit plug-ins that finally get 64bit versions). Check you plug-in vendors to see if they have 64bit versions to which you can upgrade.
kirk