Nov/Dec trip to Germany

From my experience, lodging for Xmas market cities can get booked up by June. So my suggestion is to firm up an itinerary soon, so you can secure places to sleep asap.
The markets in Lucerne are smaller and open later in December than the German markets.
The Rothenburg markets are smaller, altho I love the town .
Strasbourg and Colmar are magical .
We went to Stuttgart from Strasbourg, and enjoyed the wonderful Esslingen markets outside the city. The Stuttgart markets are great, altho they don't get much press, and quite large.

Mrs Jo here is the Xmas market expert, see if you can Search for her extensive recommendations.
I would favor Salzburg over the Munich markets.

Have a wonderful and enchanted trip!

You might want to think about traveling to Gengenbach in the Black Forest. You can easily get there from Munich, and it's a short 40 minute train ride to Strasbourg from there. I stayed there for 4 nights in 2022 and absolutely loved it. The town is very charming with beautiful half-timbered houses (it's frequently called a "chocolate box" village) and has a beautiful Altstadt, with quite a few restaurants and cafes to choose from. Gengenbach makes a good base as it is right on the main train line.

One nice benefit if you stay there is that you receive a KONUS card, which entitles you to free public transport throughout the Black Forest region. There are many charming villages in the region that you can visit along the Black Forest Railway, and there is also the Vogtsbauernhof (open-air museum) that is a joy to visit and easily accessible by train. https://www.vogtsbauernhof.de/en

The town church (Saint Marion) is quite beautiful, and the medieval gates to the city are really interesting. The Benedictine Abbey is also worth a visit, and behind it are some cloistered gardens that were a joy to wander through. This was one of my favorite places. It was peaceful and inviting and I could have stayed for hours. There were little signs of inspiration scattered around, and some children from a nearby kindergarten playing on one side.

Also don't miss a walk through Engelgasse and Höllengasse streets (near the TIC). Here you will find cobblestones and half-timbered houses, flower pots and cats resting on doormats and quaint dolls in the window. I felt like I had walked back in time when I strolled through these quaint and narrow streets. There is also a nice hike you can take that will get you above the town with some absolutely beautiful views of below. The hike ends up at a church called St. Jakob auf dem Bergle that sits above town. The TIC in town will have maps showing you how to get there. it was a really nice hike and as I said, the views are just lovely!

This is a good website for finding interesting places in the Black Forest. https://www.black-forest-travel.com/places-of-interest/

I forgot to add the wonderful advent calendar that Gengenbach has. It's a giant calendar on their Rathaus (town hall) that changes every evening. Here's an article that describes it. I think it would be well worth seeing. https://www.npr.org/2024/12/01/nx-s1-5208955/the-german-town-with-a-magical-advent-calendar-thats-as-big-as-a-town-hall

I would include the markets in Stuttgart and in Esslingen, as well as Strasbourg and Colmar (not on the weekends, as these 2 are packed)

Gengenbach makes sense as a final stop prior to Strasbourg. Freiburg is a good idea too. Stay in Gengenbach, make a day trip to Freiburg.

In between there and Munich are good options on the Romantic Road and along the Danube River...

Augsburg (RR town; town walk, daily market)
- day trip to Landsberg am Lech (RR town; town walk, daily market)

Donauwörth (RR town on the Danube, Thurs-Sun market)
- day trip to Neuburg an der Donau (RR town on the Danube; town walk, Thurs-Mon market)
- day trip to Harburg (RR town; castle, town walk) and Nördlingen (RR town, town walk, daily market)

Additional stays/visits along the Danube are possible in Ulm, Sigmaringen and other towns on your way to Donaueschingen, a Black Forest town where the Danube springs from the earth and heads to the Black Sea. From Donaueschingen one of Germany's more scenic and dramatic railways takes you straight to Gengenbach - the Black Forest Railway:

https://www.black-forest-travel.com/places-of-interest/black-forest-railway.html
https://upload.wikimedia.org/wikipedia/commons/4/4d/Verlaufskarte_Schwarzwaldbahn_%28Baden%29.png

We have revisited most of these towns in the last two years, but stayed in hotels... can't help with apt. suggestions, sorry. Karls Hotel in Sigmaringen has a remarkable riverside setting with a superb view of Sigmaringen Castle and was exceptional in other ways as well.

A few years ago we visited the Freiburg Christmas Market for 2 days . It was fairly large and attractive.

We really liked walking around the scenic town. Sadly, We had wet weather and could not see the surrounding hills. We did like the mosaics in the sidewalks.

Nice shopping zone if that matters.

A lot of great places have already been listed, so I just address the weather. Sadly, this time of the year is mostly dull, wet and grey in Germany except for sufficiently high altitudes - of which there are not that many. Black Forest and Swabian Alb (not Alps) can work, but are far from safe bets.
If it is really important to you, my best advice along the way would be the northmost alpine ranges. Consequently, I’d say you can make a short trip from a place on the East shore of lake Constance or the Allgau area. Not too familiar with their Christmas markets, though. They are on the way, more or less.
Castles and nice towns are easily found along the way though, regardless where you decide to go along.