I have seen this problem many, many times over the years. The cause is almost always roaming profiles. When users log on, the entire contents of their roaming profiles are copied to their machine. If their profiles contain a bunch of documents or other files, then all of those files have to be copied to the desktop before the logon can complete.
Other causes that I have also seen involve severe network latency and an overloaded domain controller. If you are not using roaming profiles, then I would suggest using Performance Monitor to see if anything looks out of the ordinary.