There are a few places with the Mr. Potato head station- one in each park, POP century, and Once Upon a Toy in DTD. DTD has the biggest selection of Potato parts.
Note: You do not have to buy the actual Potato Head-- just fill the box with all the special pieces! Also, you don't actually have to BRING your Potato Head to the store. Just bring it with you on your trip if you want to play with it while you're at Disney World.
If you do want to buy the Potato Head there, be sure to open it up and fill it with parts. Buy the arms! Make sure you get a left and right arm... The arms are special and can hold a lot of the props (mickey bar ice cream, suitcase, etc)
I too love filling the boxes with parts. It's such a challenge to get as many pieces as possible in the box. I've bought 3 or 4 so far and there are still a lot of pieces I don't have. They've been coming up with bigger, bulkier pieces, so it's difficult to really jam a box full.
Our AC Moore now has a make your own Mr. Potato Head section. Same idea as Disney, but no special Disney parts. Still fun, and cheaper.
The My Little Pony station has been there for several years. It's also in Once Upon a Toy-- in the back room with all the Princess stuff. There's one in ToonTown too. I'm going for the My Little Pony box this year, since DD3 is crazy about them now.
Each box costs $18. You can ask CMs for help in stuffing the boxes. They seem to enjoy the challenge too.
You can check ebay for pics of many of the pieces.