As far as I recall, it's been left as a rather amorphous a rule, but can be boiled down to how the transfer took place - simply, it doesn't always apply. I think at this point you've seen most of them:
- Walter's doorway
- How the shapeshifters cross over (Left ambiguous; I don't think this one has been seen onscreen)
- How Bell brought Olivia to the twin towers at the end of season one (Left ambiguous; I suspect this was by way of harmonic vibrations, but as far as I recall it was never stated)
- Harmonic vibrations as in 2x19, The Man From The Other Side
- Olivia in 1x19, The Road Not Taken
- The bridge - not the one from 2x19. You haven't seen this yet.
Now for the semi-spoilery part. Only "semi" because I don't think this is going to spoil the story, but I also don't think it's stated until later (if it even was stated explicitly at all):
Walter's doorway causes the most damage in the barrier between the universes - the main reason it was used so little. It defies the laws of physics in each individual universe by bridging them, and does not follow the equal-mass rule.
Olivia's method is the safest, but only possible because she was treated with Cortexiphan as a child. Although never actually stated, later episodes make it appear to be a more controlled version of Walter's doorway, and also does not follow the equal-mass rule.
The harmonic vibration method from The Man From The Other Side is the safest that can be done technologically. It can be done in one of two ways: Send an object to the other side (in which case the universes will automatically balance themselves), or swap objects between the two sides (as was attempted in the mentioned episode).
An important note is that when the universes automatically try to equalize their mass, it doesn't happen immediately. In one episode (I forget when exactly), Walter describes his experiments with Bell in regards to it - in one case, the universes didn't equalize until hours later. So some instances - like how Bell brought Olivia to him - could have simply been too rapid for automatic equalization to take place.
This part (about the bridge) is story-spoilery:
The bridge between the two universes is like a super-powerful version of Walter's window. Indeed, it's nearly outright stated later on that it's an extension of his Doorway technology, so the equal-mass rule doesn't apply to it, either.