Try resetting your preferences as described in the FAQ.
You either have to physically delete (or rename) the preference files or, if using the Alt, Ctrl, and Shift method, be sure that you get a confirmation dialog.
This resets all settings in Photoshop to factory defaults.
A complete uninstall/re-install will not affect the preferences and a corrupt file there may be causing the problem.
It could be bad TWAIN or WIA drivers, Printer drivers, corrupt fonts, buggy plugins (has happened twice), etc.
The most command hang at launch is due to printer drivers timing out (we're just asking for the default printer name and basic information - we have no idea why some drivers sit and twiddle their thumbs for 20 minutes, but they do).
TWAIN is no longer installed by default in CS4, but could be a problem if you installed the TWAIN plugin.
WIA is active by default, but doesn't cause problems that often.
If you have a lot of fonts, especially a lot of off-brand or freeware fonts - one or two bad ones could cause a serious slowdown (as our font parsing tries to make sense of them).
Corrupt plugins usually crash, but we've seen a few buggy plugins do nasty things at launch (one tried to contact a server for activation - that got fixed PDQ).
That's all I can think of offhand.