"CiscoWorks LMS" is used up to the latest release of LMS 3.x which is LMS 3.2.1
starting with LMS 4.x "CiscoWorks" is replaced with "Cisco Prime" to mark a new generation of their management software.
So you'll find "CiscoWorks LMS 3.2.1" and the latest release as "Cisco Prime LMS 4.1".
The obvious thing -from the perspective of LMS- is that the GUI has changed immensely between LMS 3.x and LMS 4.x. and there is a different way and sense how the collected information is presented.
All the latest releases of Ciscos' managment software is now published under "Cisco Prime" (e.g "Cisco Prime NAM")
the VPN Management Solution was "CiscoWorks VNM" which is EOL/EOS:
http://www.cisco.com/en/US/prod/collateral/vpndevc/ps5739/ps2330/prod_end-of-life_notice0900aecd80653315.html
http://www.cisco.com/en/US/products/sw/cscowork/ps2330/index.html
as a replacement "Cisco Security Manager" (CSM) should be used - but I am not sure if it has the same features like VNM. You find some infos here:
http://www.cisco.com/en/US/products/ps6498/products_documentation_roadmaps_list.html
http://www.cisco.com/en/US/products/ps6498/tsd_products_support_general_information.html
http://www.cisco.com/en/US/products/ps6498/prod_software_versions_comparison.html
CSM is a security application and focused on Firewall management, VPNs and has Policy-based Management features where as LMS is for network management and monitoring. They can not replace each other even if they have a few overlappings.
