One known culprits is Parallels (if you have or ever had that installed). VMWare may also cause similar problems, but the list is endless and its not necessarily going to be the same for everyone. Try to get some clues as to what is causing the slowdown by doing this:
Open Console.app by clicking on Spotlight in the top-right of the screen and typing 'Console', then press 'return.
Look in the sidebar under 'FILES' for 'System Log' and click on it.
Click the 'Clear Display' icon in the taskbar, and then 'Insert Marker'. Make a note of the time on the marker.
Press the power button once to display the shutdown window. Make sure 'Reopen Windows when logging back in' is selected. Shutdown the computer (not 'Restart').
When the computer is off, press the power button again and log in. The Console window should be at the front of your screen. Skim through the messages and look for any obvious hangs or repeated messages.