If I am on a flash heavy website, and I clear my browser cache, the site continues to function.
Chances are the entire swf is not loaded into flash's active memory at the time I clear the browser cache (especially for sites that use large rsl libraries such as papervision3d). I can verify this with flash-builder's profiling tools.
So, where are the swf libraries kept on disk (or in memory somewhere else?) which allow the site to continue to function?
Naturally the browser will not clear files that it is actively using, that would really be sawing off the branch you are sitting on.
Flash does however use the browsers cache for all regular files. So the files will be stored in the same manner as the rest of the cache. Exactly how this works when you clear the cache with a flash app running depends on the browsers cache implementation.
RSL's are different since they are cached by the Flash player itself, likely in one of the directories Kitsune mentions.
Maybe it's not the cached swf but other cached data. Flash has a mechanism similar to cookies to store local data. Right-clicking the flash object and then setting the storage size to 0 deletes that data. Then set it up again and the "cookie" for this site is removed.
Not sure if this is the data you're looking for, but on Windows, Flash Player stores some information in %APPDATA%/Adobe/Flash Player, %APPDATA%/Macromedia/Flash Player, and %TEMP% (the last being where .flv files are stored, although they're named with a .tmp extension, and at least on my system look like they start with a 'fla' prefix).
On Linux, I'd try checking in ~/.adobe, ~/.macromedia, and /tmp, or variations of those, and I'm not sure of the equivalents on OS X.
The flash profiler does not show all of the memory use of a swf.
http://forums.adobe.com/message/2138309
and
http://blogs.adobe.com/aharui/2008/09/using_the_flex_builder_3x_prof.html