If you don't want ClickOnce, then you'll probably need to create your own MSI. In that case, you can use:
- The built-in Setup project type in Visual Studio. It does a decent job but has limitations. Works very well if you don't have many dependencies or custom actions.
- A commercial tool like InstallShield
- WIX (Windows Installer XML)
I've tried both 1 and 3. While WIX has a little bit of a learning curve, it is a very rich way to do what you want to do. There is a fair bit of documentation available and some very nice "out of the box" wizard sequences to handle your standard install scenarios (licenses, feature selection, dependencies, etc). WIX does have some VS integration that works quite well.
You can find out more on WIX at http://wix.sourceforge.net/
Note:
The VS setup project can do custom actions, and install dependencies, but you have to use custom actions. If you want to parameterize the custom actions, then you'll need to find the not-so-intuitive instructions on that topic.
The other limitation of the VS setup project is that the setup project can only be compiled to an MSI by VS (devenv.exe). That means that the MSI cannot be compiled on a build server unless you install Visual Studio there too. This was a show stopper for me, so I switched to WIX and was very happy with the result.