Applications Hang at Launch

I'm having a problem launching Applications - any application. When I click on the application icon in my dock, it bounces and bounces but never gets the little white dot that signifies that the application is open. After a while it will stop bouncing. But, then it appears that the system thinks that the application IS open, and I have to Force Quit the application to try to open it again. Applications that open on start-up are fine.
I am running the console and am getting the following reports no matter what application I launch (these particular examples came when I tried to launch the Disk Utility:
10/19/10 10:09:01 AM com.apple.launchd.peruser.501[94] ([0x0-0x2f02f].com.apple.DiskUtility[295]) Bug: launchdcorelogic.c:5845 (24108):9
10/19/10 10:09:01 AM com.apple.launchd.peruser.501[94] ([0x0-0x2f02f].com.apple.DiskUtility[295]) Bug: launchdcorelogic.c:5846 (24108):9
10/19/10 10:09:01 AM com.apple.launchd.peruser.501[94] ([0x0-0x2f02f].com.apple.DiskUtility[295]) Bug: launchdcorelogic.c:3663 (24108):9
I have Verified and Repaired permissions several times. There are three permission repairs that seem to return over and over. It says that it is repairing them, but they still show up on the next scan.
I am dumbfounded. Please help.

Ugh! I'm so frustrated!
The problem isn't consistent so it's hard for me to explain what's happening. When I tried to isolate a problem in the prefs, I moved all the prefs to a folder on my desktop, then started moving them over a little at a time and trying to launch apps as I did that. I had only moved over a few prefs when I started having the problem again. So, I moved those prefs back to the desktop, but I still couldn't launch. I kept trying to isolate a problem there, and I couldn't make sense of it - it was all inconsistent. Eventually, I decided to Restore the Prefs from the back up that I did yesterday before all my problems started. That seemed like it might be helping because I was able to get a few apps to launch. But, I was still having trouble with other apps. Sometimes one app wouldn't launch, so I would force quit and try again, and then it would. Sometime an app would launch fine. I would quit and try to relaunch and then it would hang up. Other apps just wouldn't launch at all. I restarted the machine again, and could only get Disk Utility and Safari to launch before I started having problems again. I'm just at a loss. I feel like I'm going to have to restore the whole computer, and I've never done that before. It scares me. What else can I try?
Just an FYI, this is what I get when I repair permission in Disk Utility:
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar".
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/readconf ig" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/writecon fig" has been modified and will not be repaired.
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib".
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
It's exactly the same every single time I have run Repair Permissions. I don't know if it means anything, but I think it's weird that I get those exact same permissions with problems every time, and it says that it repairs them every time, but they are still there the next time.

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