That is... UNTIL TODAY. Because Rifftrax has just announced the RiffPlayer, a program for both PC and Mac that synches up your Rifftrax and your DVDs perfectly! I actually got to try it out last week, and it works fantastically. All you have to do is make sure you open your DVD in the RiffPlayer (not your computer's regular DVD program), find the RiffTrax mp3 and the new sync file, and the program figures it out from there. And if things do happen to slip off track, there's a "resync" button right on the control panel that fixes things instantly. And you can even adjust the audio levels of both the movie and the Rifftrax!
Seriously, it's fantastic, and I can't recommend it enough. There is one caveat, though -- not all RiffTrax currently work with the RiffPlayer (there's a full list here). But a lot of previously released titles do -- all you need is those special sync files, which Rifftrax is offering for free here if you've previously purchased the mp3 for a compatible title.
Oh, and did I mention the RiffPlayer itself is totally free? Or that if you download it you get a free Rifftrax?
Seriously, go here, download the RiffPlayer, and improve both your Rifftrax and your quality of life immensely. If you liken Rifftrax to the invention of the wheel -- which I do -- then the RiffPlayer takes the wheel and turns it into a car. It makes Rifftrax more enjoyable, easier to use, and it allows you to stop when necessary. No RiffTrax fan should be without it.