This website has compiled quite a lot of cool secondhand/vintage shops. It's in German, but is updated with descriptions, store addresses, hours and directions. It also lists them according to "genre"--vintage design, clothes, furniture, etc. Very handy web guide. http://nichtneu.ch/was-suchen-sie/kategorie/4

Lux Plus is great for vintage clothes and accessories. Caritas is good for more modern second hand. Blenda Vintage has some cute items, but tends to be overpriced and they are super unfriendly. The Kanzlei market on Sats. (even in winter, although smaller) is also great for vintage clothes and design.

For those in Zug, there is a wonderful upper-scale second hand shop called Ka 2, right by the big post office off Poststrasse. They sell mainly luxury brands, similar to luxury-shops.com, but are MUCH less expensive.

Happy hunting!