It may suprise you that I find a couple of things slightly better in the 2003 version of Sharepoint than the 2007 version. One thing is that consistency (and the lack of ;)) of navigation. In SPS2003, you could alert yourself on almost anything (the link was always there!). For example, you could alert yourself on changes of an area. So if a document was added to a document library that was placed on that area you received an alert. Even better was that when a subarea was created, you received an alert that a new area had been discovered!
Now it could be me but I haven't found this 'feature' yet in 2007 (MOSS/WSS), thing that comes close is the searchresult alertme functionality. So if anyone knows where I can find this piece of functionality in 2007 please let me know!