I'm seeing this phenomenon on multiple sites, but to take one page in particular,
http://www.slate.com/id/2225617/ . Every few seconds Safari creates empty files like /Users/Desktop-1-1 and empty directories like ~/Desktop-1. Safari stops doing this as soon as I close the page.
The fact that Safari is writing files in the filesystem outside its cache, let alone reading them, shows that something is possibly seriously broken with the JavaScript/Flash sandbox security model.
Turning off JavaScript is just not an option on today's Web.
Safari 4.0.3, Shockwave Flash plugin 10.0r32, Mac OS X 10.4.11, PowerPC G5.