Via Twitter Diablo, comments from Bashiok that Waypoints will work in Diablo III the same way they did in DIablo II:

Blizzard: Waypoints

Updated waypoint UI design and implemented. Waypoints will function similar to Diablo II.

Let's remember that Dialbo III also has the Checkpoints mode, which is very similar to other RPG-Action games like Titan Quest.

Waypoints were seen in the Blizzcon demo with a new look, where one of them led to a dungeon. It is foreseeable that it was implemented and we really will be able to move through the world of Sanctuary. It look something like this: