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So, I'm pretty new to Mac and I made a very big beginner mistake... I gave myself permissions to the entire harddrive. 18 hours later I eventually got it to run "DiskUtil repairPermissions /" and the system appears to be stable.

Now... I believe this problem is related to the fact that my admin account still has rights to everything. Multiple applications are not retaining their settings. Adium forgets my notification settings, Eclipse keeps asking for the workspace path, MonoDevelop forgets my layout, Chrome forgets that I want the OmniBox to use Instant search... and so on.

Does my .config folder have the wrong permissions? Is there something else entirely I don't know anything about that I need to fix? I know it'll probably take some terminal commands and I understand the basics of chmod and how permissions work (ish). Any ideas would be appreciated.

Edit:

I'm being more cautious about things now. I have a better understanding now than when I started and won't make any changes that I don't see as necessary.

Currently I still have permissions over everything that Repair Permissions didn't reset permissions for. I still have read/only permissions over the root folder, the applications folder, and /Library. I'm skeptical of just removing myself from the harddrive for fear that it might remove my permissions from EVERY file.

Considering how bad I messed this up, things are running stable (aside from the preference amnesia here), I'm writing this from the machine.

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Please don't go messing around with system internals when you're this new to the system. – Daniel Beck Jan 24 '11 at 18:28
I certainly don't intend to be so forward with my learning next time. I'm usually more cautious than this question might lead you to believe. Either way, I know I messed up big time. – Corey Ogburn Jan 24 '11 at 18:41
Your permissions at the moment sound fine. Your personal application permissions are in your home folder, not /Library or /System/Library. You might find this completely unrelated answer and the linked Apple documents interesting. – Daniel Beck Jan 24 '11 at 18:51
How did you "give yourself permissions"? I.e. did you add your account to the Permissions list in the Finder's Get Info window (and then "Apply to enclosed items"), or go to the command line and chown everything to yourself, or something else? – Gordon Davisson Jan 24 '11 at 22:59
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Your personal configuration is stored in ~/Library/Preferences, where ~ is /Users/username/. The file name convention is like java packages with reverse domain names, e.g. com.apple.Finder.

Check the permissions of the paths to these files.

If you changed the location of your home folder (System Preferences » Accounts -- don't!), your preferences likely did not move from that location, and you're starting from scratch (I haven't used it before). You can try copying the files.

If you enabled FileVault (encrypted home folder), it's possible that something went wrong when you mounted your home folder. Are the preferences good again when you log out and back in?

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I haven't changed my home folder and I don't intend to do so. Should I remove my personal permissions from ~/Library/Preferences? ~/Library? /Library? I am not using FileVault. – Corey Ogburn Jan 24 '11 at 18:40
If there are personal preferences, and you have permissions, then it sounds fine. Are the modification dates of some of these files (those for the applications you're currently using) very recent, i.e. a few minutes ago max.? – Daniel Beck Jan 24 '11 at 18:49
No... Oddly enough the files are 2 days old. Although I'm not sure what's causing this, those are probably the preferences that my applications are reloading every time they "forget" my new preference changes. Any ideas? – Corey Ogburn Jan 24 '11 at 18:59
@Corey Are all those files two days old? If no file is more recent, something's wrong. Quit your applications. Zip a few files for third party applications you installed (e.g. com.google.Chrome.plist) and delete the original. Start Chrome, it should be back to default settings. Quit Chrome. Is a new preference file with that same name created in its place? – Daniel Beck Jan 24 '11 at 19:04
Not necessarily all, there are some apps I haven't used since before 2 days ago and those applications' plist files have modifications dates earlier than 2 days ago. After deleting adium's and chrome's plist file (after properly backing them up) it has placed new plist files with this instant's date/time. I've learned from my mistake, I'm not going to just start deleting without an opinion on it, but would that solve it? – Corey Ogburn Jan 24 '11 at 19:12
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As an addendum to other users, as of Snow Leopard you can boot to the installation media (DVD, or thumb drive if on a new MacBook Air) and reset your home folder permissions via the "Reset Password" utility. You would select your internal drive, choose your user, and click the "Repair Permissions" button. There is no need to actually reset your password.

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