Why, after installing the CS6 update, are all the old CS3 apps still in the Applications folder?

New versions of Adobe software do not install over the top of old versions. They're installed side-by-side, each version in its own folder.

You can have several different versions of the same software installed simultaneously (I have CS3, CS4, CS5 and CS6 available), in case you have old plugins not compatible with newer Adobe versions or you simply want to maintain access to old versions for forum troubleshooting or whatever.

If you're certain you're never going to need the CS3 versions again, you can safely uninstall them.