We met them in front of the castle last June. There was no EE at that time, so this was right at 9am opening on a Sunday morning. We were one of the first hundred or so people down Main St. and just as we made it to the "hub", Minnie and Mickey came out to greet, autograph, and pose together. It was a wonderful experience for the whole family on our first morning of the kids' first trip!
The only other place we saw them "together" was at Chef Mickey's, but they don't actually pose together. At the MK we have pictures of the whole family with BOTH Minnie and Mickey in the shots.
Also, I would suggest being one of the first people into "Toontown". That is usually about 10am and has it's own rope drop. There are usually lots of characters out there early, and the lines are nonexistant at the "judges tent" area. We managed about 6 or more autographs/pictures in the first half hour in that area last June.
Finally, just keep your eyes peeled, as characters can appear almost anywhere at any time. Some of our best character moments happened this way (like Kermit and Miss Piggy).