They are likeliest to put this new IS in an L zoom. The telephoto primes are either (1) too new to justify a redesign, and/or (2) too expensive to see any significant sales boost from implementing the new IS on them. Add in the fact that Canon does not have IS on any prime lenses below 200mm focal length, and you see how unlikely it is that they will debut the technology on a prime. Zooms are ideal because they are popular and more tolerant of compromises (primes are scrutinized very harshly as they are expected to be extremely sharp corner-to-corner).
Next, IS tends to be featured on longer zooms; e.g., 24-105/4L IS (which I believe is the widest EF lens with IS), 70-200/2.8L IS and f/4L IS, 28-300/3.5-5.6L IS, and 100-400/4.5-5.6L IS. There's no doubt it will be an L zoom receiving the new IS, and I doubt it will be on the 70-300 DO (it doesn't sell enough to justify it), the 24-105/4L IS is too new, and the 28-300/3.5-5.6L IS is not really popular enough nor is it optically as good. So that pretty much leaves the 70-200/2.8 and the 100-400/4.5-5.6 as the candidates to receive this new IS.
I think in light of this announcement, the 70-200/2.8 is going to get it. In fact, I think BOTH are going to get it. We just haven't heard the rumors about the 100-400 because it's flying under the radar and being overshadowed by the buzz around the 70-200.