I totally agree with you about the thrift stores in town, there is not much to be found (unless you get really lucky). I didn't know that cycle analyst sells used bikes, so I'll check them out. Fly Bikes is the only shop that showed up in my online searches for used bikes in the Denver area, but I haven't found anyone that has experience with that particular shop (I guess I'll go check it out).
I'm not interested in anything super nice, just something that fits well and isn't as clunky as my current mtb. Buying from a shop that can help me get a good fit on a used bike would be my first choice (as opposed to buying off of craigslist, and then taking it to a shop...it would be nice to get a deal on any changes in parts, and necessary maintenance)
I'll let you know what I find.