Hi Mark
Cisco recommends not using vlan 1 for any user/management traffic. Where i work we have a dedicated vlan for managing the switches. No port is left in vlan 1. In addition we always set the native vlan on trunks to be vlan 999 otherwise it will default to vlan 1.
Vlan 1 is still used internally by the switches for vtp, pagp, stp traffic. You can't stop this happening but you can make sure you don't use it yourself.
Attached is a link on a vlan security paper from Cisco which covers the use of vlan 1 among other things
http://www.cisco.com/en/US/products/hw/switches/ps708/products_white_paper09186a008013159f.shtml
HTH
Jon