I am looking at putting together a trip to Austria/Switzerland/Germany (I would consider a quick trip over toward France if it warranted it and I want to visit some great wineries that are making really good wine that are not the "major labels". If anyone has some thoughts or experiences, it would be greatly appreciated as my searching has yielded few results.
My favorite German wine region is the Mosel River Valley along the Mosel River. It's absolutely stunning and dotted with more wineries than I can list both large and small. It starts around Trier and winds all along the river to Koblenz. Bernkastel-Kues and Cochem are both larger towns along the route that offer a lot of wine tasting opportunitites. You can easily spend a day or two driving along the Mosel from Trier to Cochem (and beyond) stopping at various tasting rooms.
Unfortunatey, I don't have a favorite to recommend, but if you get there, you'll find several that you like and many small labels to choose from.
For a really special place to stay, go to Burg Pyrmont and stay just below it at the Landgasthof Pyrmonter Mühle. It's a wonderful little bed and breakfast with one of the best meals I ever ate along the Mosel.
Mentioned in this answer:
I'd recommend wine tasting through the Rhine Valley. You can even take a boat ride up and down the Rhine River and get off in various towns along the way for wine tasting.
There's also Bad Neuenahr-Ahrweiler. I spent a few weekend in this beautiful place in the spring time when I live in Bonn. An old medieval town with vineyard on hills surrounding the town. From what I remember it was primarily pinot noir if you're into that. Enjoy!