I have two machines upgraded to Win 7 from Vista.
On both machines there have been problems installing and particularly upgrading odd bits of software - but not neccessarily the same on both machines. So for example, on one machine Java works fine. On the other Firefox says that a java plugin needs to be installed, but then it won't install.
They all seem to be access and permissions issues - and I suspect that the software installer wants to use some folders that Win 7 thinks it shouldn't be accessing. For example the Microsoft uninstaller wouldn't install because it needed access to a folder in the c:\users\username\.... path.
But beyond that I'm mystified.