Do you know whether you should use Click Once or MSI?

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Check the following table whether ClickOnce is suit for your application.
This table compares the features of ClickOnce deployment with Windows Installer deployment. Read ClickOnce Deployment Overview for more details

Feature	ClickOnce	Windows Installer
Automatic update¹	Yes	Yes
Post-installation rollback²	Yes	No
Update from Web	Yes	No
Does not affect shared components or other applications	Yes	No
Security permissions granted	Grants only permissions necessary for the application (more safe)	Grants Full Trust by default (less safe)
Security permissions required	Internet or Intranet Zone (Full Trust for CD-ROM installation)	Administrator
Application and deployment manifest signing	Yes	No
Installation-time user interface	Single prompt	Multipart Wizard
Installation of assemblies on demand	Yes	No
Installation of shared files	No	Yes
Installation of drivers	No	Yes (with custom actions)
Installation to Global Assembly Cache	No	Yes
Installation for multiple users	No	Yes
Add application to Start menu	Yes	Yes
Add application to Startup group	No	Yes
Add application to Favorites menu	No	Yes
Register file types	No	Yes
Install time registry access³	Limited	Yes
Binary file patching	No	Yes
Application installation location	ClickOnce application cache	Program Files folder

Notes

With Windows Installer, you must implement programmatic updates in the application code.
With ClickOnce, rollback is available in Add or Remove Programs.
ClickOnce deployment can access HKEYLOCALMACHINE (HKLM) only with Full Trust permission.

Customize the Installation of the Application, including: Publish location, installation url, install mode, publish version, Download files on demand, Prerequisites, Updates, Options.