This is a little old, but for any future people that find this thread, I thought I'd add a summary about it afterward, since there's some conflicting information above. I want to prevent confusion about the results....
It should leave the screen blank for the whole frame, and as long as you still do Vsync you should be okay. I can't speak for every single TV, but this seems fine to me.
I did some experimentation and this worked fine. I'm using it in my game. I just leave vblank on, but keep the vsync timing correct. It draws a blank frame, which is exactly what I wanted. This answer seems right on.
It's probably not a good idea to leave vblank on. For changing screens just turn off vsync until you're ready to start the frame. Doing this every frame would never be a good idea, as it could make a dark frame in-between all other frames(causing a flicker effect) but just between scenes and stuff like that it should be fine.
This had very bad results. (and was what caused the problems in the first place) Turning of vsync until I was ready to start the frame meant that I had an uneven frame rate, which caused the screen to roll. Unless I'm misunderstanding what gip-gip is recommending, this answer is just incorrect.
Using every other frame decreases the frequency of the video signal to 30 HZ; there are half as many frames, the emulator creates dark frames where none exist.
This doesn't really relate to what I was asking.