Judder is almost never a problem with the source unless maybe you're watching something that was mastered from film (screen shake) or the encode was poorly filtered (bad IVTC). Otherwise, it comes from your display's refresh rate not being an even multiple of the video's frame rate.
For example, if you watch a 30 fps video on a 60hz display (which almost all LCD computer monitors are), 60 / 30 = 2, so every frame is displayed for 2 screen refreshes and you get smooth motion with no judder. But most anime is 24 fps, so you get 60 / 24 = 2.5. And what happens when you switch frames mid-refresh? Massive screen tearing. Because screen tearing is ugly, you use vertical sync to force frames to only be drawn in sync with the screen refreshes. Thus, you get frames displayed in a 2-3-2-3 pattern of refreshes, which creates judder since the frames aren't all being displayed for the same amount of time.
The only way to get rid of judder without any side effects is to change the refresh rate of your display.