Apps won't sync to my iPhone 4?

Prior to upgrading to iOS 6, I did not have my apps synced to my iphone via iTunes because I had been using different laptops every few months and didn't want to go through the hassel of redownloading certain apps.
When I upgraded to iOS 6, I had none of my apps(which was expected) so I went on iTunes and downloaded a few apps I needed and then synced my iPhone. All my music, photos, etc were synced but the apps weren't. I have 'Sync Apps' checked but all the apps are unchecked so I checked them all and synced again but again, they didn't sync, they just became unchecked.
I also have 'Automatically sync new apps' checked.
I also can't seem to download any apps from the iTunes store via my iPhone.
I haven't been able to find much on the issue and having no apps is starting to get very annoying.

First of all, do you still have the old iPhone 3? If so it's pretty easy to then do a transfer.
Failing that, whilst you may not have sync'd the contacts to the computer (possible) they should be stored within any backups that were created of the old iPhone. You can head into iTunes and go to Edit -> Preferences -> Devices tab -> Backups and check for the list of previous backups.

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