If you religiously monitor each installation with tools like Ashampoo Uninstaller or Total Uninstaller, you can easily wipe out everything that gets installed, including registry entries. I use Ashampoo and try to monitor each new installation.
Not a panacea in my experience - often applications build dependencies based upon the order in which things were installed (which is why sometime trying to uninstall an MS hotfix will wran you that it could break a specific list of applications that were installed after the Hotfix). The trouble with AU and TU is that they are blunt tools...
I'm about five months late responding to this, but what the heck: I actually use Ashampoo Uninstaller to monitor the installation of software which I'm not sure that I am going to keep. I uninstall applications using Windows built-in removal feature or by going to the program's folder and directly running its "uninstall.exe" file. Usually, this is all I need to do. If I have subsequent problems - recalcitrant shell menu entries, for example - I can then view the Ashampoo Uninstaller file. This will list all of the changes made to the registry, and serves to guide me to entries specific to that application. This makes it easy to identify keys associated with whatever problem I am trying to sovle, almost invariably either orphaned context/shell menu entries or file extension assignments, so that I don't have search through my entire registry. Beyond this, I tend to ignore orphaned registry entries. I don't much care if there are keys left behind if they don't impair the operation of Windows or other software that is still on the computer.
I totally agree with Carol, though: I no longer use Ashampoo Uninstaller to uninstall anything, for all of the reasons Carol detailed. I did want to point out the utility of being able to track changes that a software installation makes to your system, though. Ashampoo Uinstaller allows me to target specific changes and make corrections. I don't, however, advocate using it as intended, which can lead to serious problems. Of course, there are free alternatives out there, I *think*, that provide similar functionality.
EDITED for clarity... (success?!).