Yes, I use wix, I have to admit it's not the easiest tool in the world, but it does give you a fair bit of flexiblity.

I have an example of how to place a short cut on the users desktop on my blog here.

My top tips are for using wix are:
Use virtual pc to test you're deployments, that way you can use undo disk and start with a clean image each time.
Always install msi's using msiexec -lv* log.txt -i my.msi, because the logging info gives you alot of insight into how to do things. It is partically useful for working out the syntax for well known directories.
Use orca (part of the windows platform sdk installer section). This has a very useful validation feature
Use dark to reverse engineer msi to look at how other people do things.