As you may know the security features have been completly revamped for WSS 3.0 comparing to WSS 2.0 (for good reasons), as part of this change during migration each WSS 2.0 Site group within a site gets mapped to a custom WSS 3.0 Permission Level and all the members will be added individually as SP users with equivalent rights. This major change in security and lack of understanding of new security features in WSS 3.0 could confuse and in some cases frustrate SharePoint admins after the migration. The following Microsoft support article explains this in detail and provides some sample code to convert WSS 2.0 Site groups to Cross-Site groups before migration as by design Cross-Site groups get converted to WSS 3.0 SharePoint groups. 

http://support.microsoft.com/kb/938110/en-us

There is also another great article which explains all the migration steps in great detail:

http://support.microsoft.com/kb/938110/en-us