Application won't be installed after canceling "restore from backup"

I just recently updated my firmware from 3.1.2 to 3.1.3. So what I did was restoring it to factory settings and update its firmware. Afterward, I attempted to restore my IPhone 3G from backup that I made before.
In the process of installing back all previous applications, I received a phone call and I answered it. So that results in canceling the sync of application installation from backup. With that action, I had to redo all those things (restore to factory settings) again and restore my data from that backup. Unfortunately when I finished restoring from that backup, my applications are all gone. What should I do?

Are the Apps in iTunes? If they are just sync the phone.
If they are not then download them again, you will NOT be charged.

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