The biggest difference is that Selenium has support for different browsers (not just IE or FF, see http://seleniumhq.org/about/platforms.html#browsers.
Also, Selenium has a remote control server (http://seleniumhq.org/projects/remote-control/), which means that you don't need to run the browser on the same machine the test code is running. You can therefore test your Web app. on different OS platforms.
In general I would recommend using Selenium. I've used WatiN few years ago, but I wasn't satisfied with its stability (it has probably improved by now). The biggest plus for Selenium for me is the fact that you can test the Web app. on different browsers.
