Simply put, first choose a course, then the university. Since the backbone of the Swiss economy is industry, pharmacology and banking, the most in-demand studies are engineering, economics, IT, technical, mathematical, and social sciences.
For technical disciplines we recommend the Federal Polytechnic School of Lausanne (EPFL) and the Swiss Federal Institute of Technologies (ETH), for economics and business the University of St. Gallen (HSG) and Bern University of Applied Sciences, for banking and law the Universities of Lausanne and Fribourg, for humanities the Universities of Zurich, Geneva, or Lausanne. You can get a good art or architecture education at the University of Basel, at ETH or at the University of Bern.
The second important point when choosing a university is the language. You know and want to improve your German - it is taught at the Universities of Basel, Bern, Lucerne, St. Gallen, Zurich, and ETH. For French, choose the University of Lausanne, Fribourg, Geneva, Neuchâtel or the EPFL. The University of Lugano is recommended for Italian.