What I am worried about is NT SP6a messing up the other fixes I have installed since I did that one. My install order has been over time

NT4
SP6a
IE5
Option Pack (for PWS, MTS, etc.)
Office 2000
SP6a
MDAC
MS Java update
Sun Java runtime environment
Visual Studio
Visual Studio SP3
Office 2000 SP1
Several Office 2000 hotfixes (how do you uninstall them btw?)
Visual Studio SP4

And in between I have been to windowsupdate.microsoft.com several times to get lots of fixes. What I suspect is that I will apply SP6a, it will overwrite several hotfixed DLLs from other, later service packs (Office, VS, windowsupdate) but the Registry entries for the hotfixes will show that the hotfixes are still there.....

>SP6a contains all the stuff in the previous SPs. You shouldn't need to install another after that.