How to recover non-app-store Software?

I am trying to restore my iMac to the factory settings. Currently it is running the latest version of OS X Mountain Lion.
Here's the problem. I have a bunch of Non-Mac App Store Software installed in it and I wonder how am I giong to restore them after the system reinstall. I know there should be no problem with App Store purchases as I can D/L them later. Would non App Store S/W work if I copied them to a different external drive and then copied them back after system reinstall?

Archive your existing system: Use Time Machine to back up or "clone" your existing system to another volume, using Carbon Copy Cloner or equivalent utility.
Restore your iMac to factory settings using its original System Install DVD or OS X Recovery whichever is applicable.
Using Setup Assistant, migrate your archived User Accounts and Applications to the restored iMac.
This will ensure the complete transfer of your previously licensed software.
Following that, upgrade your iMac to Mountain Lion using the same Apple ID used to purchase it. You do not have to pay for it again.

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Please read this whole message before doing anything.
This procedure is a test, not a solution. Don’t be disappointed when you find that nothing has changed after you complete it.
Step 1
The purpose of this step is to determine whether the problem is localized to your user account.
Enable guest logins* and log in as Guest. Don't use the Safari-only “Guest User” login created by “Find My Mac.”
While logged in as Guest, you won’t have access to any of your personal files or settings. Applications will behave as if you were running them for the first time. Don’t be alarmed by this; it’s normal. If you need any passwords or other personal data in order to complete the test, memorize, print, or write them down before you begin.
Test while logged in as Guest. Same problem?
After testing, log out of the guest account and, in your own account, disable it if you wish. Any files you created in the guest account will be deleted automatically when you log out of it.
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Step 2
The purpose of this step is to determine whether the problem is caused by third-party system modifications that load automatically at startup or login, by a peripheral device, by a font conflict, or by corruption of the file system or of certain system caches.
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The login screen appears even if you usually log in automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.
Test while in safe mode. Same problem?
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If your Mac is not allowing you to download 3rd party apps that are from a source other than the Mac App Store, it is likely the security setting in System Preferences. Go to Sys Prefs/Security & Privacy/General and set the download options best for you. You will likely find the download options grayed out. You will need to click the padlock below and supply your admin password to unlock the preference pane.

My mac app store has disappeared from my dock and when i pull it up in finder it says it is damaged. how can i download the mac app store software?

my mac app store has disappeared from my dock and when i pull it up in finder it says it is damaged. how can i download the mac app store software?

Delete the App Store app by dragging it and dropping it into the Trash. Then download and install the appropriate update combo for your version of OS X;
Install new MAS app -
OS X Mountain Lion 10.8.3 update combo
http://support.apple.com/kb/DL1640
OS X Lion 10.7.5 update combo
http://support.apple.com/kb/DL1583
OS X Snow Leopard 10.6.8 v1.1 update combo
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I have App Store 1.0. MacUpdate Desktop tells me there is a new version 1.0.1. How do I update App Store. Mac Update only takes me directly to App Store. Not much help in that, as I don't find how to update the App Store itself.
Regards
Guttorm Kittelsen
<Edited by Host>

Thank you for your advice.
Actually, I am aware that the upgrade is implemented in 10.6.7. However, up until now I haven't been able to upgrade to Mac OS X 10.6.7, as I have software that is not yet compatible. So I wondered how to do it within 10.6.6? May be it is not possible? Anyway, this gave me a push to track the software I use for compatibility, and I found that an update for 10.6.7 now is ready for download, so then I will probably solve two issues at the same time. Takes a little work though. Thank you again for your advice.

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How to recover non-app-store Software?

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