"Zermatt and the Matterhorn"
Why does anyone go to the crowded, expensive, and touristy Zermatt? See the photo above -- that's why. No doubt, there are a number of disadvantages, not the least of which its isolated, "dead-end" location at the end of a 2-hour private railway that doesn't accept Eurailpasses (Swisspasses ARE accepted, however). When the weather is bad, there really isn't a lot to do, and most would be well advised to go elsewhere. When the weather is fine, however, the hikes and views are among the best in Europe. My favorite place to stay is the Hotel Weisshorn, which, while not cheap, is a reasonable, friendly, and comfortable place to stay.
"The Bernese Oberland and Kandersteg"
Certainly my favorite area to visit in Switzerland is the Bernese Oberland. While most people like to visit the Jungfrau and its famous resorts of Grindelwald, Muerren, and Interlaken (and of course the Stevesian Fundamentalist pilgrimage destination of Gimmelwald), I prefer the ambiance of the area one valley over in Kandersteg. While Kandersteg is no secret, it's just far enough off the beaten path to keep away from the tour bus crowd. It's a pleasant mix of backpackers, hikers, hang gliding enthusiasts, Swiss vacationers, and independent tourists enjoying a pleasant vacation from reality in idyllic surroundings. Kandersteg is easy to get to by car and rail, and has a wide variety of accommodations. My favorite hotel-restaurant is the Bernerhof, though many others swear by the Hotel-Restaurant Adler next door.
"Appenzell and the Seealpsee"
A bit off the beaten path is the canton of Appenzell-Innerrhoden. While its capital, Appenzell, is very famous and can be a tourist zoo during peak season, the area at the end of the line of the Appenzell Bahn is much less so. If you continue on to the village of Wasserauen (itself little more than a wide spot in the road), you have the opportunity to visit some less-travelled areas and some beautiful scenery. There are a pair of mountain huts on the Seealpsee, about a 40 minute hike from the train station (NOTE: the trail to the Seealpsee is very good, but some may consider the climb extremely steep and strenuous. Pack light.). We stayed at the Berggasthaus Seealpsee, right on the lake. From the Seealpsee, you have some great hiking opportunities to the nearby Ebenalp, the famous Berggasthaus Aescher, and even up to the peak of the Säntis if the conditions are right and you're in good shape.