Installing to an empty directory is best. For example, I used:
Program Files\jv16 PowerTools 2006-beta2
Program Files\jv16 PowerTools 2006-beta3
Program Files\jv16 PowerTools 2005
Program Files\Power Tools (jv16)
and can have all four versions up at the same time with no problems caused by that.
jv puts out a tight package!
Of course, doing this, I exercise due care when launching tools, considering function and order, and rename the jv16pt shortcuts so I know which one I launch. :)
I also use different names for the start menu folders, to simplify uninstall.
You should be all right with the registry. The only ones I find for jv16 2005 are MRU and MENUORDER related. You may have some setup history in yours (harmless) and DisplayName and UNINSTALLSTRING entries, also harmless since 2006 install will replace them.
Bottom line for your case: uninstall 2005, use an empty directory with a distinct name for the new install (Program Files\jv16 PowerTools 2006 recommended), no jv16 registry entries of concern.