I would start by finding the UninstallString in the registry for the particular app you want to uninstall. I am running Vista x64 so my results are different than I remember. I remember it being HKLM\Software\Microsoft\Windows\Current Version\Uninstall where all the products where, but on Vista x64 it appears to be HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Installer\UserData\S-1-5-18\Products\.

In each product there is a UninstallString Value that you can use to uninstall products. For example, to uninstall Quickbooks 2007 it is MsiExec.exe /I{71EEA108-09C9-4D81-8FA2-D48C70681242}. You would just need to do some searching on Msiexec to find the silent switches and then use shell to run it.