I recently found $100/night in SF tough, even with FF hotel certificates. As I recall, best I could do was an average of about $190/night at the big chains with one of those puppies. But I was staying an odd number of nights, which makes the 2 for 1 certificates a bit less valuable.
A couple of other suggestions. You might try one of the Joie de Vivre (spelling? sorry if it's wrong) or Kimpton hotels; these are two local chains of small boutique hotels, some of which are pretty nice. I stayed at the Rex, which is close to Union Square, for about $140 a night including breakfast. These places are atmospheric, small and quirky, and can be fun, but are perhaps not the best if you need a full range of business services.
Second, try 1800hotel.com, a hotel consolidator. When I went earlier in the spring, they were offering the Crowne Plaza for $149 a night. In retrospect, I wish I would have taken this offer -- it's a big hotel tower right by the Rex and I probably could have gotten Priority Club points.
Charlie