Using the new Hoppers in Update 1.5, I made this Automatic Potion Brewing Machine.

You just have to load hoppers on top full of the ingredients (signs tell you which ones go where), and fill another hopper with water bottles, and it is ready to go. You can just go down in front, pick the type of potion you want, choose if you want it stronger, increased duration or if you want it to be a splash potion, and press the start button. About 2 minutes later, three of that potion will be in the chest at the front of the machine for you!

This works but using hoppers the fill a brewing stand with water bottles and the ingredients to brew the potion you want. A piston loop timer (using the new redstone block) is used to drop out the right ingredients in the correct order to make the potion. There is a large glass wall that allows you to view the items being dropped into a stream of water that takes them to the brewing stand. A tone plays when the machine starts, and when it is done, as well as a light indicating that the machine is running. There are additional warning lights that how if you are out of water bottles or other ingredients, with lights at the filling area showing exactly which ingredients are missing.

Additional Notes

The schematic is just the basic machine itself. It can be made into a building, and already has internal stairs to get to the filling platform (and a door can be put before these stairs). From the loading platform, there is a small stairway (which again can have a door placed in front of) that leads to the water flow and ingredient storage chests which can be used if maintenance is needed (accidental loading of an ingredient into the wrong place).