safari 4b does improved quite a bit in its download manager since safari 3.x
but still, even in safari 4, you still dont get to choose downloading destinations for each download, which means if you download a lot of stuff of different kind, safari will put them all in the same folder.
There is also no search function in safari 4b that you can easily locate items in your download list, if you were to have massive amount of downloads.
safari still does not support ftp download, it will redirect you to finder when you try to reach a ftp server. Which isn't exactly a good way to go.