In my case it is Excel
I have this problem too and I think I have narrowed it down to a problem with Excel (and maybe Office generally) I have Office for Mac 2011. If I open, modify and save a file, I get the same shutdown problem. In fact I don't know if the spinning wheel ever stops. I have left it as long as 15 minutes before using the power button to shut down. If I open a spreadsheet and close it without saving, I do not have a problem. The problem seems to be tied to the save function.
To test, I downloaded OpenOffice and had the same problem.
If I force a power down using the button, startup seems a little slow but I have not measured this. If I do a second restart right after the first, it is normal. I have tried sessions without Office (Firefox, iTunes, Quicken Essentials, etc.) and never seem to have a shutdown problem if I do not save in Excel. I have not tested for the other Office applications.
I seldom do a full shutdown, but this is still a disturbing problem. I was going to post this with Apple but I am thinking maybe I should post it with Microsoft.