I've owned both. The dock version is a pain to deal with because you must remove it from your case every time you want to use it. I use a case called Yoobao magic case now and it works great with the Bluetooth keyboard because it props up to the perfect viewing angle and I just start typing away. Any case that allows the iPad to be propped up at an angle for viewing (and there are a growing number of them) will be a perfect match for the Bluetooth keyboard. I sold my dockable keyboard on eBay immediately after I realized the complexity of using it with a case.
BTW, if you have an iPhone with iOS4, you can use the Bluetooth keyboard with it too.