http://msdn.microsoft.com/smartclient/default.aspx?pull=/library/en-us/dndotnet/html/clickoncevsinstaller.asp
ClickOnce是.Net 2.0的一项功能。它的主要关注点是在具有安全的运行时环境下的智能客户端的简单的基于Web的发布。
而Windows Installer是传统的Windows程序的发布工具。
该文给出了ClickOnce和Windows Installer的功能矩阵，如下：
| Task | ClickOnce | Windows Installer |
|---|---|---|
| Install Files | X | X |
| Create Shortcuts | X | X |
| Associate File Extensions | X | X |
| Install Services | X | |
| Install to GAC | X | |
| Manage ODBC | X | |
| Manage COM+ | X | |
| Write to Registry | X | |
| Advertising | X | |
| Self-Repair | X | |
| File/Folder/Registry Permissions | X | |
| Install-time User Interaction | X | |
| Install for All Users | X | |
| Custom Actions at Install/Uninstall | X | |
| Installation Conditions/System Interrogation | X | |
| Auto-Update and Scheduling | X | |
| Forced Updates | X | |
| Security Sandboxing | X | |
| Download/Install Assemblies on Demand | X | |
| Rollback to Previous Version | X |
可见ClickOnce和Windows Installer各有长短。Windows Installer具有更多的Windows的系统级的安装能力，而ClickOnce则具有更灵活和更便捷的安装体验。因此，该文最后还给出了结合两者的应用程序发布方案。