Tonight, I tried putting my G5 to Sleep Mode, but it hung around for about 30 seconds to actually go to sleep.. I took it out of sleep mode, and tried it again after fixing permissions. Same thing. What's going on? There are no programs open
So what, if the problem is in the drives catalog checking permissions won't do squat.
Running Disk First Aid and fsck will check the drive for quite a few of these problems, although neither of them fix everything in one pass.
If there is a problem with the file system/catalog, you'd see some slowdown when you dump stuff to the HD -- and sleeping is dumping stuff to the HD.
Booting into "Safe Mode" is OS X's equivalent to booting with extensions off that we had under OS 9 (heck it even uses the same key to do it). So don't knock it til you try it.
If there is a problem with something you are running, it should help you point it out -- like a .kext file for some widget you may be running that's causing problems.