Stupid question here...but anyway.. If I compress my pages with ob_start("ob_gzhandler") What affect would that have on flash files that are compressed?
Flash files? Like .swf? Lol, those are not a part of your PHP code. Using ob_start("ob_gzhandler") only the output of the script itself will be compress with gzip. Like images Flash is loaded separately- the browser makes another GET call to the server for it. In other words, no effect at all. Though if you are looking for a way to compress your swf files then just look on Google, there are alot of different tools out there designed just for that.
Flash can be compressed by the webserver, but don't think you will save alot of $$ on compressing them. Most servers compress there data on the way out! ask your host if you want to know more!