WSS = Windows SharePoint Services
SPS = SharePoint Portal Services
SPS gives you much better search functionality, meaning it can search throughout the portal and within sites. It's also context sensitive meaning it won't search stuff you don't have access to. You can also extend its search engine to index sites outside of SharePoint.
It's an actual portal, you can figure out what to do with it here. In this you can automatically categorize sites for easy access.
It's easier to manage because you can see usage details at a site collection level. WSS is just one big site collection. This helps because if you keep on creating sub-webs, you can't easily see usage analysis and decide if this site is no longer needed and needs to be archived.
SPS has MySite, which allows users to have their own little section with all their Alerts from different sites in one spot as well as other things.
You can read more here:
Comparison of features that are included in Windows SharePoint Services and in SharePoint Portal Server 2003