With "ClickOnce", running a Windows Forms application is as simple as clicking a link in a web page. Deploying or updating an application is simply a matter of updating files on a server; no need to individually touch every client. ClickOnce has the requirement pre-requisite of .NET Framework 2.0 or above which is listed on the default pre-requisite items including other runtime packages, windows installer engines and so forth. Through deployment, this becomes easier as we can create a single package with required pre-requisite along the application. However, we can only add those prerequisite through ClickOnce which are by default in prerequisite list while publishing.
To add your own (custom) prerequisite you need to have a boot strapper package. Amol Malpani at codeproject has some simple steps to create your own boot strapper package which will then be automatically included into the prerequisite list. Author guides for how to create custom pre-requisites by using "Bootstrapper Manifest Generator". If you were struggling how to create such a package, this article is worth a start: Add your own custom pre-requisite to ClickOnce Applications
Amol also has other related articles recently published discussing about Publishing an Applicaiton using ClickOnce, without VS 2005 using Mage UI utility and Restore Application to Previous State using ClickOnce