There is now an extension from Chrome that allows you to launch a click once app (ClickOnce for Chrome).
Unfortunately it does not update the user agent so it is impossible to know if the site will support it. There is a way to change the user agent in Chrome, but it's not something I would expect average users could do. However, here is an answer on the Chrome help forums that explains how for reference.
Basically create a shortcut to Chrome and add this command-line parameter to the target.
--user-agent="Mozilla/5.0 (Windows; U; Windows NT 6.0; en-US) AppleWebKit/534.10 (KHTML, like Gecko) Chrome/8.0.552.224 Safari/534.10 .NET CLR 3.5.21022; .NET CLR 3.5.30729; .NET4.0E"
You might want to make sure you have the current user agent. Here is a site that will display it for you. The part you will want to add to the user agent is ".NET CLR 3.5.21022; .NET CLR 3.5.30729;" (of course this might also depend on what is installed on the machine).
Another downside to this approach is that it does not appear the modified user agent is available in Javascript (I'm still getting the unmodified version).
------ EDIT ------
If you want to know if ClickOnce is available on the client, here is a Javascript function I wrote that will tell you...
this.hasClickOnce = function () {
var userAgent = navigator.userAgent.toUpperCase();
if (userAgent.indexOf('.NET CLR 3.5') >= 0) return true;
if (window.clientInformation && window.clientInformation.plugins) {
// check to see if a ClickOnce extension is installed.
for (var i = 0; i < clientInformation.plugins.length; i++)
if (clientInformation.plugins[i].name == 'ClickOnce plugin for Chrome') return true;
}
return false;
};
