After a complete uninstall, there are various entries left behind such as mstr.hist, mstr.bhv files (these two files depict the installation and license key history on the machine) from the Common Files folder, log files, etc. Likewise, some registry keys will remain.
The cleanest way to perform an uninstall is to go to Control Panel > Add/Remove programs and choose 'Remove All' in the maintenance dialog box. This uninstalls the entire product suite, but certain files and registry entries will remain. In these cases, there should be no need to manually delete them. In fact, Strategy strongly recommends that the registry entries are not deleted. Upon re-installation, these files/entries will be appropriately over-written, where required.
To summarize, an uninstall from Control Panel > Add/Remove programs followed by a reboot of the machine is the optimum method prior to a re-install.
Note: Any Strategy Web customizations will not be retained in the case of an uninstall followed by a re-install (including over-installs). Therefore, it is highly recommended to back-up the Web directory.