Is it the "example" watermark?
If you're using iShowU HD Pro and you see the demo watermark overlay you can delete this by selecting the image and pressing delete.
If hitting the Delete key does not work for you, click the watermark once to highlight it, then from the iShowU menu bar at the top of your machine choose Edit/Delete, and the watermark should disappear.
If you see a watermark on compressed video, it could be for a couple of reasons.
The Stomp "demo" watermark looks like this (it's burnt into all encoded video when in demo mode):
If you see some other watermark, the chances are that you're seeing a watermark from some third party codec. A good example is the 3ivx Codec which places a huge red watermark over the entire video. If you see a watermark that's different to the one above then it pretty much guaranteed to be from some other source (aka: check your third party codecs). To remove any iShowU/Stomp watermarks you need to unlock your software.