Measuring and visualing web application performance using apache logs?

Well, this misses one of your requirements (not FLOSS), but try Splunk. It's free (as in beer) for up to 500 MB of data indexed per day.

It makes it trivially easy to get the kind of data you're looking for; statistical reporting on the response time drilled down to a certain URL, or aggregate reports of what the fast and slow URLs are, would be a breeze.

Why not look at New Relic (http://www.newrelic.com)? It can do that sort of reporting, live even, and much more. If has a free Lite version which still covers what you want even if don't want to pay out money for more introspective features.

Disclaimer. I work there and that is the project I am working on right now. I trust you are however also enjoying my other project called mod_wsgi. ;-)