We'll officially find out soon enough, but right now I expect that Nintendo isn't deviating much from the DS cartridge design. I would expect that 3DS cartridges are roughly the same size with the big difference being that they would be keyed differently from DS cartridges. You would end up with something similar to the GBA cartridge slot, where it could accept GB games but the GBA cartridge was different enough (not counting the fact that it was shorter) that it wouldn't fit in a GB.
Nintendo could remove the notch that the DS uses, but that would make it possible to put a cartridge in backwards. They could also make 3DS cartridges slightly wider on the right side so that they couldn't fit in to a DS. The locking mechanism is on the left and the notch is on the right, so the notch would keep DS cards aligned and pushed up against the locking mechanism.
Nintendo could remove the notch that the DS uses, but that would make it possible to put a cartridge in backwards. They could also make 3DS cartridges slightly wider on the right side so that they couldn't fit in to a DS. The locking mechanism is on the left and the notch is on the right, so the notch would keep DS cards aligned and pushed up against the locking mechanism.