One of the main shortcomings of ClickOnce is the inability to install GAC related items, and to execute addition installation requirements such as creating registry settings.
To accomplish this you must create a custom Bootstrap which is installed as part of the pre-requisites. This is easier than it sounds. In essence :
Create a project which includes all the references required.
Create an installation project that loads the references into the GAC (and does other pre-requisite actions)
Copy the msi to the boot strapper folder for Visual Studio (e.g. C:\Program Files\Microsoft Visual Studio 8\SDK\v2.0\BootStrapper\Packages or C:\Program Files\Microsoft SDKs\Windows\v6.0A\Bootstrapper\Packages)
Create a product.xml to identify the msi.
*Update - make sure you create a subfolder to hold the language specific EULA. Without this it will break!
Alter the Prerequisites in the click once publish tab to include this new project.
There are some nice articles on this, not least some example code from dasBlonde.
Also :
Installsite bunch of links
MSDN bootstrap manifest generator
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