Missing Apps after System restore

Yesterday I did a System Restore on my iPhone 3Gs and now all of my Apps are missing. After this I tried to do a Restore from backup again but I still have the same problem.
I don't have Sync Apps ticked in iTunes as if I do it will sync all apps and there is a mix of iPad and iPhone apps there. For some Apps there are separate iPad and iPhone versions and I'm not sure if this will cause any problems.
Is there a way to have the apps restored to the same folders they were in before? I know I can sync selected apps from iTunes but I spent a lot of time organising all of my apps into folders and I'm hoping to avoid having to do that again. When I tick "Sync Apps" but before actually going ahead iTunes shows 10 screens of Apps and none are in folders as they were before.
I thought that doing a restore from a backup that I did just before the restore would have restored the phone exactly as I had it before.
Thanks for any advice you can offer.

No iTunes content including 3rd party apps are included with your iPhone's backup. If you don't have Sync Apps selected under the Apps tab for your iPhone sync preferences with iTunes along with the apps selected below that you want available on your iPhone - which can be placed in folders with iTunes followed by a sync, iTunes does not know which apps you had installed on your iPhone. With Sync Apps selected along with the apps in your chosen folders, when restoring your iPhone with iTunes from your iPhone's backup, your iPhone will be restored in this regard. After restoring as a new iPhone or from the backup, this must be followed by a sync to re-transfer your selected iTunes content including 3rd party apps to your iPhone. What is selected under the Apps tab for your iPhone sync preferences will be pre-selected prior to the initial sync with iTunes after the restore, and the apps will be transferred back to the same folders as before. Your mistake in this process was not having Sync Apps selected under the Apps tab. With this selected, after downloading an app direct with your iPhone the app will be copied to your iTunes library automatically the first time you sync your iPhone with iTunes after doing so.
If there is an iPad only app that you select to be transferred to your iPhone, a warning message will be provided with the following sync indicating the app cannot be installed on your iPhone. You can create your app folders with iTunes followed by a sync.

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