How do I migrate apps from an old iphone if I didn't back them up

How do I migrate apps from an old iphone if I didn't back them up?
I created a backup of my iphone 5s just before activating my iphone6.  But I chose not to back up the apps to my computer because at the moment I was thinking of my MBA's hard disk space.  Now that Im restoring the backup to my new phone, I get an itunes message saying 64 apps were not installed on my phone because the apps could not be found.
The phone is still restoring photos.  What can I do to get those apps on my phone without having to re-install them manually?

Ok, I have my old iphone5s and my new iphone6.
I have apps on my iphone5s, i haven't erased anything.
One of those for example is iBank.
I connect the iphone5s to my mac, in iTunes I select the phone, click on Computer backup "This computer" and click on Backup now.  Itunes says its backing it up and finishes.
Now I unplug the iphone5s and plug in the iphone6. 
It starts to sync but then gives me an error saying some apps were not installed:
The games I don't care about, but iBank I do, there is also a company erp app.  Those are the only 2 I really need to have back on my new phone.  No matter how many times i backup the old, it just won't find the apps.  Why?

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