Some people have their favorites and enjoy the heck out of the markets, and then there are those who find it doesn't matter cause they feel like they are all the same. I am in the former category and search out markets that have their own unique flair and that offer more handmade items.
Smaller towns may be just one weekend and you get a cosy atmosphere due to the surroundings. Towns like Idstein, Gelnhausen, Tübingen, or Büdingen. Then there are medium sized towns that again due to the architecture surrounding the markets make them unique. Marburg, Seligenstadt, Mainz, Heidelberg, Bad Homburg and Rüdesheim. Others are unique due to their themes. Esslingen is one of my favorites as it is medieval, making it completely different. Stuttgart, though a large market is spread out in such a way and decorated so lavishly that it is also unique as it is a lot more fun walking through this market than a packed market. Large towns will have multiple markets spread through the city, all with different themes. You find this in Berlin, Cologne, Munich and a bit in Frankfurt.
Stuttgart was the only town offering goose bratwurst and the planked salmon being served in a giant, Finnish tipi with open fires keeping us warm as we sat on fur covered benches was a special treat. Taking the chair lift up to Germania standing watch above Rüdesheim at close to dusk offers a stunning view, with the decorated town below and the lights of the ships going past. Mainz has huge wine vats to sit in, with tables seating 6, and with a bonfire in the middle of the circled wine vats, all under the shadow of the 1000 year old cathedral. Büdingen, like Rothenburg, is a medieval walled town located an hour away from Frankfurt, and their market is just on one weekend, but the town is so pretty with the decorations on the walls and towers and fachwerk houses. Idstein is just plain gorgeous as is Marburg, with the entire town filled with fachwerk houses and beautifully decorated. Seligenstadt offers an indoor market on 2 weekends that takes place in the ancient Abbey begun by Charlemagnes biographer, Einhard. Here you will find the most beautiful hand made items, with the artists and craftspeople who made them on hand, some of them creating while they wait.
I would also consider going to the markets in the East, like Erfurt, Seiffen, Lübeck, Quedlinburg, or up to Potsdam. Loved the French markets in Strasbourg and Colmar.
I hope to visit the ones in Salzburg, Cochem, and Trier this year.
My short visit to Munich during the market left me unimpressed. Though nice enough, there wasn't anything really special about it. I could have been anywhere.