I am now booking hotels for a trip to Switzerland in September 2014, staying in Luzern, Muerren, and Lausanne. When I went to the hotel's own web booking tools, or to sites like Hotels.com and Booking.com, I was getting both high rates and low availability. (I need a single, but many hotels only had much larger and more expensive rooms like deluxe doubles, triples, and quads available). This particularly applied to Luzern and Lausanne, where I truly despaired of finding anything affordable (I'd like to stay under 150 CHF per night, and ideally around 120 CHF, per single room per night). The Ibis hotels in the centers of these cities looked a bit depressing, but at least they had room and were affordable, so these were my last resort.
However, I e-mailed all the hotels I was interested in, saying that I found out about their hotel from Rick's book and asking about availability and rates. WITHOUT EXCEPTION, all of them had rooms available that weren't showing on their websites, and/or offered lower prices (in some cases, the Rick Steves discount that would only be offered with direct e-mail booking). In Luzern I'm paying 130 CHF; in Muerren 95 CHF; and in Lausanne 125 CHF (not including the 2-3 CHF room tax in Luzern and Lausanne).
So, if you're looking at hotels in Switzerland, don't use the booking sites without checking directly with the hotel first, and don't assume the room you need is not available without checking directly with the hotel. While this is always good advice, this is the first time I've seen it so uniformly, in multiple hotels in multiple cities.
And if anyone has any idea why Lausanne and Luzern are so full in September, let me know!