Permission query.

I went to replace a utility that needed to be updated (the printer repair utility) but when I dropped it into the app folder it wouldn't let me replace it because I didn't have permission. It did not ask for authentication!
I know I could change the permission of the single app trash it then drop the new app in. But I wanted to sort this problem out once and for all.
The permissions on the repair utility were owner: unknown Group: Admin.
Some other apps like photoshop are owner: System Group: admin.
I changed the permissions on the Application folder to owner: System Group: Admin But when I checked 'apply to enclosed items' it said I didn't have permission even though I'm an admin user.
So I have two questions.
One. Can I use terminal (read: what is the full terminal command) to force all the permissions and ownership in the app folder to be Owner: me, Group: Admin then do a repair permissions to change all the system apps back to Owner: system.
Two. Is there any problem if all the my own installed apps in the app folder are set to Owner: system Group Admin.
I'm the only user of the computer.
emac   Mac OS X (10.4.6)  

What does 'DU' mean.
My plan was to make all the permissions in the app folder to be 777 and the owner to be user and the group to be admin, then I was going to do a repair permissions to return all the System apps back to their normal permissions thus leaving all my own apps with me as the owner.
I could do all this by hand one app at a time but there are 124 to go through. I was hoping there was a terminal command to do this.
The reason the permissions are screwed is that this computer was once mine but it is now my wifes and she is the sole admin. I'm just wanting to make all the permissions to be what they would have been if she was the original owner and installed all the extra apps herself.

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