ClickOnce didn't work well for us. We install the database on our customer's server. The database on their end needs to be updated before we do an update. We have a lot more than just 2 or 3 customers, so doing ClickOnce for our application is not really the best idea, unless I am missing something important about ClickOnce.
What I did, was add a field to the database for version number. On our ftp site, I have a versions folder that has a folder for each version number of our application. Inside that particular version's folder, we put a zip file with the setup.exe and the msi file that the setup.exe will launch. All the pre-reqs are downloaded from the vendors site to ensure that our FTP site isn't getting hit with huge downloads (.Net 3.5 when we moved to it). When our application launches, it checks the field in the database for the version number, and if it's different than the current versions assembly version, it will connect to the ftp site, download the zip file from that new version's folder, unzip it, and execute the setup. This will install newer versions of .Net or any other requirement we may have added, then launch the MSI to install our application and all the user has to do is click next a few times.
