First of all, there are two flavours of Messenger available. You have MSN Messenger (now in version 7.0 beta) which is the public version, and you have Windows Messenger (now 5.1 available) which is the one you will use if you setup your own IM infrastructure within your company using Office Live Communications Server 2005. Windows Messenger 5.1 has a number of improvements you can read here. Notably some faster performance when integrating with SharePoint.