MSI packages are the windows installer package. Older programs used to have the setup.exe package, but most of the newer programs today, have MSI packages, replacing setup.exe.
For the programs that have MSI packages, you are able to assign them or publish them using group policy. Assigning an application installs it on the machine and it appears in the start menu. The application installs automatically upon first use.
Publishing an application only makes it available to install, but it's up to the users to choose if they want it. It'll appear in add/remove programs in the control panel.
check out the following link for more information
http://www.microsoft.com/windows2000/en/advanced/help/default.asp?url=/windows2000/en/advanced/help/appmgr_editdeploytype.htm
remove any spaces from the URL.