Alright. I see two major ways that people use watermarks.

The first way is by taking your profile pic and dropping it into the Branding feature for your watermark (You should first make it a PNG and then make the background transparent. Not necessary, still effective either way).

The second way is to utilize it as a Call-to-Action by having it display either Subscribe or Like, etc.

What do you think is the better option? Do you see any other forms of effective watermarks? Comment them.
I usually do both.
During the video I'll have my logo as an overlay over the video in the corner and at the end of the video I'll use my logo as the subscribe "button". Now that YouTube has updated their endscreen annotations this sort off happens automatically anyway because as soon as you add the subscribe function, I'll add your avatar from youtube.

I'll probably also start using my logo on my thumbnails, just to try and enforce my brand a bit more.

Other than these, I wouldn't know of anything else to use a watermark.
I like the call-to-action bit, though I really don't know how it affects viewers' behaviors.