As John Potts noted above Apple ripped the RSS functionality out of Safari v6 (and probably the reason for that is that they removed the underlying RSS functionality from OS X in Mountain Lion) - unfortunately the Top Sites refresh page notification uses RSS to determine whether a page has been refreshed so it's axed as well.
There's a couple of other threads on this and this is what I've found:
Just like the removal of RSS for v6, this missing Top Sites indicator functionality is a feature of v6.0 (not a bug, unfortunately).
Both (RSS & Top Site indicator) have apparantly been gone since the first beta of Safari v6 (which was called v5.2 initially) according to folks who used the betas.
Here's the page where the folks discuss this in the comments:
http://www.macworld.com/article/1168016/bugs_and_fixes_troubleshooting_mountain_ lion.html
This also squares with the fact that Safari v5.1.7 crashes immediately on Mountain Lion (if you copy it to another directory in Mountain Lion), but runs fine on Lion. Mountain Lion has had the RSS plumbing removed at the OS level, while Lion still has it (which is why Lion can run Safari v5.1.7 and still has Top Site update functionality and RSS functionality working).
So where does that leave everyone? If you're running Lion and want that functionality, copy Safari v5.1.7 (from Time Machine or a Mac that still has it - Snow Leopard macs still do) to a separate directory in the Applications directory and you can get back your RSS and Top Sites update functionality (for the time being). Never run both versions at the same time or you can have file corruption since they share bookmarks etc..
If you're running Mountain Lion it looks like your stuck loosing this functionality (short of rolling back to Lion and using v5.1.7 until a better solution comes along - which might be worth it to some folks).
I haven't been able to find any other browser that has this situational awareness indicator of site updates - if anyone knows of one please post it. All the other browsers have thumbnail images of sites but nobody else indicates if updates have occured. What a bummer, my favorite feature of Safari was killed off intentionaly...