In researching Bohemia, I've been intrigued by the Karlovy Vary region, and especially the area around Loket, which from what I can see from photos and online trip reports has the magical combination of a cute (though small, I realize) old town, a castle, verdant forests, and is near a very beautiful section of the Ohre River valley. Some of the photos from that valley are stunning, indeed one of them is my screen saver right now. I'd like to hear from others what areas, anywhere in Europe, they've seen have such a combination, and if not with a river, a lake instead.
You know what's funny, Rob? When I saw the headline for your post I wanted to suggest Loket. I was there just last June. Well, you already know about it. It (together with Karlovy Vary) made it to the last edition of Rick Steves book: Prague & the Czech Republic. You are absolutely right; it's pleasantly quaint, untouristy; can you imagine I was the only guest in the hotel which could accommodate about 30 to 40 people. The owner himself made my breakfast according to my wishes, one of the best I ate in any hotel. The town got some similarities with Cesky Krumlov - river from three sides, town and castle on the hill, little square, winding streets around. I saw several houses for sale for fraction of price what it would be in Cesky Krumlov. Why am I not rich or skillful with trades (houses needed some renovations) I immediately asked myself. I visited Cesky Krumlov in 1975. It was run down then but I saw the potential and sure enough it even exceeded my expectation. I see the same potential for Loket to become another Cesky Krumlov (well, almost). My recommendation is don't postpone your visit if you want to see it still as quaint untouristy town.
I am sure there are other areas with similar combos but we don't know them. Because if more of us know about them they are no more untouristy - Hallstatt, Zell am See (true, they don't have a castle). What about Altfinkenstein (nearby Villach) - old castle or improved ruins of old castle, very little town and it's above a beautiful lake with even more beautiful name Faakersee (yes, it's pronounced the same as you think).
My first thought was of Chateau de Chillon, a castle on Lake Geneva and near Montreux and Vevey.
Hohnstein in Germany near the Czech border is similar to Loket. The town is smaller and less impressive, but the mountains/forests are better. The castle, a inexpensive B&B with good reviews, sits high above the Polenz valley in the middle of Saxon Switzerland (you can hike from Hohnstein to this view), probably Central Europes best hiking region. If you follow the Polenz valley you reach the Elbe river, from where you can take a paddle steamer to Königstein fortress, Pillnitz castle, Pirna, Dresden or Meissen.