I considered using both. I used the recorder for Selenium to build some tests in FF. I tried to do the same in Watin and found that the Watin Recorder (2.0.9.1228) is completely worthless for our sites. It appeared to be rendering the site in IE6 -- making our site effectively unusable for recording. We don't support IE6. I couldn't find any way to change the browser it is using. I only found one Watin Recorder out there. If there's more than one, or one that is kept up to date, please comment.
The Selenium Recorder IDE for Firefox is simple to use and ports tests to C#. It isn't great at this. I couldn't get porting test suites to work, despite reading a blog post or two that had workarounds. So there's a bit of manipulation of the generated code. Still, it works 90% and that's better than the alternative.
For my money/time, Selenium is superior just for the ease of building new tests. IE doesn't have any good developer toolbars that are anywhere near as good as Firebug, so I'm doing my development in Firefox to begin with, so having a good working recorder in Firefox is a huge bonus.
My conclusion here was a lot like that democracy quote by Churchill: Selenium is the worst form of automated UI testing. Except for all the other ones.