Hi Chachacha -
For small and varied meals, including lots of take-away, the Migros and Coop st0re chains often have restaurants at their larger locations and grocery stores as well as substantial buffets. For example, there is an extensive selection at the Coop store across the street from Zürich main station, near the river and the Bahnhofbrücke:
I often use their restaurants for a sit-down meal when traveling around Switzerland; many are near the main stations.
In Luzern, a walk around the old town on either side of the river will reveal plenty of restaurants that offer Swiss cheese dishes. I don't recall in the small cafes in Luzern main station offer such food. Raclette and fondue, although popular winter dishes all throughout Switzerland, are associated withe the French speaking regions, such as the Canton Valais, so a restaurant with the name "Valaisanne" in the name is often a good bet.
When in doubt about anything in Luzern, I stop at Tourist Information by track #1 and ask. I find them quite helpful, and knowledgeable.
For years, in Luzern, I have used the Restaurant Rathaus Brauerei, along the quai near the old town hall. They have had a range of foods, from simple to complex, of good quality and (for a Swiss tourist center such as Luzern), reasonable prices. They changed management in this past October, so I shall try them again when I have a chance, to see how they are now. Even better in warm weather, for outdoor eating, their inside restaurant is good for cold weather. I'd be surprised if they did not offer raclette or at least, fondues.
foursquare.com/v/ratha us-brauerei/4b9a4f3df964a 52053ab35e3
They re-open on December 10th.
In Zürich, the Hotel which I always use, the Hotel Adler, in the Niederdorf, has an extensive menu of different fondues and raclette.
Can't comment about Thun from personal knowledge.
Here is what Rick Steve's has to say about Coop , Migros, and the similar Manora. I generally don't like Rick Steve's approach to traveling, but there are enough comments from travelers in this link to give you some idea about the food at Migros and Coop throughout Switzerland