I think Steve hit the nail on the head with why people get into using prefixes.  A lot of people got used to naming their database objects with prefixes precisely because they "group together" well in Enterprise Manager and other GUI tools, so they could easily group user-defined objects for easier management.

OTOH, with the addition of schema support in SQL 2005, I think the rationale/justification people use for built-in prefixes is gone.  Schema support in SQL 2005 and how it affects naming conventions would be a nice addition to this article.