Have you tried booting into Safe Mode? Hold down the shift key when you hear the Mac startup chime. You'll know that you're in this mode as it will take a while before you get to the desktop since Safe Mode performs disk checks and repairs using fsck upon bootup into Safe Mode. You'll also see the word "Safe Mode" somewhere in the bootup progress bar once it's past the gray Apple screen with the rotating dial. Once you're in this mode, try repairing permissions just in case.
Incidentally, did you perform any updates before this happened? I know that some people had issues with the 10.4.9 Delta Update that shows up on Software Updates. Usually I just download the Combo Updater for my platform and install manually, all the while making sure that only the keyboard and mouse is connected (if it's a desktop Mac) and nothing else. Also remember that 10.4.9, like a few of the previous updates, restarts your Macintosh twice: once after you install the update and one more time after that before getting to the desktop. Some people end up losing patience thinking that something went wrong since it doesn't get to the desktop right after the first restart and end up shutting it down prematurely, hence causing problems.