I've never changed a system table, but I did change a system stored procedure in SQL 2000. I had quite a few meticulously named DTS packages which, to my great frustration, were not sorted by name when viewed in the DTS package list.

I found msdb.dbo.sp_enum_dtspackages and changed "ORDER BY id" to "ORDER BY name, id".

It was one of the happiest days of my life.