Minecraft mechanism to separate merged carts?
Here you go: How to Split Up Merged Carts
Note: This mechanism no longer works, due to water not pushing minecarts. I have filed a bug for that change in behavior: MC-665.
This design is based off of Polt's water-based splitter idea, but splits carts as fast as they can be fed and sends them on separate tracks automatically.
The water flows leftward in the first picture. Carts come in on the upper track at the bottom of the picture, drop through the water (getting pushed slightly to the left), and hit the center lower track. If there are two carts, then they rapidly push apart and land on the center and left tracks (and all boost away together).
It still needs tuning; in particular, I think more vertical distance is needed as sometimes merged carts hit the middle track together (on the other hand, I've also seen them hit the left track together). But this seems like the core of an effective solution. A refinement might be using multiple water layers to steer the trajectories further.