Use an own slide for a video and play it fullscreen. Since you want to emphasize it, you should not have it as a small gimmick in a corner of your slide. In the other case (you do not want to focus on the content of the video) it is only distracting for the audience and does not provide any added value to your presentation. In those cases it is preferable to not include the movie.
Always use a resolution that is appropriate. If you know that you will use a presenter that has a "screen" size of 1024x768 pixels than you should not include a video that is only 100x100 pixels in size. It will look very pixelated. In addition, it is not only hard to realize different objects in the movie when it is shown in such a quality but also difficult for the audience's eyes. Noone will be able to watch it over a longer timespan.
Videos are in general not a good content for presentations. The reason for that fact is that in most cases the presenter just stands idly at one side of the stage when a video is shown. Especially when the video has its own audio. But the audience is expecting a presenter speaking when they go to a talk. Nevertheless sometimes the usage of a short movie clip can be much more impressive than the same content just spoken by a presenter -- a good example for that are the product presentations of Apple: