Separate folder names with semicolons, then invert the installer and folder values:
<Project ToolsVersion="4.0" DefaultTargets="Inversionator" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup>
<Folders Include="Folder1;Folder4">
<Installer>Installer1.msi</Installer>
</Folders>
<Folders Include="Folder1;Folder2;Folder3;Folder4">
<Installer>Installer2.msi</Installer>
</Folders>
</ItemGroup>
<Target Name="Inversionator">
<Message Text="%(Folders.Installer) %(Folders.Identity) " Importance="high" />
</Target>
</Project>
Output for the task is now:
Installer1.msi Folder1
Installer1.msi Folder4
Installer2.msi Folder1
Installer2.msi Folder2
Installer2.msi Folder3
Installer2.msi Folder4