I have a solution which contains multiple executables, a widget player, a widget designer and others. My prior MSI allowed the user to run one msi and all executables would be installed with appropriate links in Start->All Programs->MyApp folder.

I would like to do the same with ClickOnce. Is this possible? If so, how?

It is very possible however because of the... simplicity of ClickOnce it's not as obvious as we'd think or like.

First you'll need to add your other executables to the project that will be deployed and set their build type to content. Next you'll want to head into your projects properties page and from the Publish tab select the Application FIles button. From the provided dialog you'd probably need to check the 'Show all files' checkbox to see all of the non code/resource files of your project so that you can add some to the install group.

I have a similar problem, but my launch app can't have the references of the other applications because this has to be configured in runtime.

It has to be able to launch any app installed, even apps not mine.