A little late, but make sure to test out your ClickOnce deployment very thoroughly in your client's environment. Omitting detail here but there are many problems with ClickOnce. I have been supporting a ClickOnce app for 3.5 years now and have run into many problems with manifests, having to manually delete the sandbox storage folders so the updates install correctly, etc. - if you search online for ClickOnce problems you'll find quite a few issues in the MSDN forums and elsewhere, many of which MS does not appear to want to resolve as they've been open since VS2005.
Also, be aware of a potential gotcha in ClickOnce prior to .NET 3.5 SP1. If you do not have your own software deployment certificate from a CA recognized by the client machines, Visual Studio uses a "temporary" certificate (*.pfx) which expires one year from creation. After that time, subsequent update releases will probably not install, and will show users scary messages about cert expiration. Microsoft fixed this in .NET 3.5 SP1 but you had to dig through the release notes to find the comments that temp or perm certs were no longer required. So - if you don't have a public CA cert, and you'll be supporting this app for some time, then make sure you're on .NET 3.5 SP1.
Depending on the complexity of your scenario, since you ask about other solutions, we wound up using a "roll your own" approach that goes something like this.
Each updated release increments the assembly version as needed.
Build contains custom step to auto-generate a file with the new assembly version.
Deployment project copies version file to the output directory with MSI.
Each time the installed app runs, it compares its own version to the version in the version file in the deploy folder. If they differ, quit the app and launch the MSI, which we set to automatically remove older app versions.
This is a "poor man's ClickOnce" for an environment where there are no app deployment tools whatsoever avl. (not even AD app advertising) so we made do. Again, this approach may not be sophisticated enough for you, but it works fine for us.
Best of luck.