WIX

I have been using WIX for a while and I must say that it is great. If you don't know, WIX stands for "Windows Installer XML". It is basically a way to script a MS installer file (.msi) using a simple XML based language. It is perhaps the best way you can possibly write a MSI file. It is free, open source, and MS has been using it for years. In fact, most of their products' installers were written with it. The second best choice is probably to buy an installation-maker such as InstallShield. However, the prices for these types are programs are generally through the roof and even then they don't offer exactly what you want. WIX is many times more powerful than any program I've seen and it has better results. MS could practically sell it; it is that good (of course, it wouldn't be as good if it wasn't free).