Safari 4’s choice for Top Sites may miss ones that you’d like included (maybe one you haven’t been to in awhile got bumped out of the lineup because you hadn’t pinned it). You don’t have to wait for it to show up on its own:
1. With Top Sites in Edit mode, open a second window (not a tab!).
2. In the second window, go to the site you want.
3. Grab the little icon in front of the URL in the address field (it’s called a favicon) and drag it into the Top Sites window.
4. The new thumbnail is automatically pinned where you let it go, although you can move afterward.
In Safari’s public beta, you couldn’t see the new thumbnail’s Remove/Pin buttons until you left the Top Sites view entirely and then returned to its Edit mode, but that was fixed in the real release.