How do I restore Apps & such from my second computer?

Itunes update trashed my iphone,  itunes and windows 7.  Then after I managed to restore my Iphone,  it deleted all of the apps on my phone and trashed Itunes on the same computer.  Itunes and any backups on that computer are no longer available.
I have a backup of my apps on another computer with Itunes installed,  but... surprise!!!! I do not trust Itunes a whole lot anymore and am afraid to try to restore those apps to my iphone.  I am afraid that it will simply do what it did before,  and delete my apps in computer backup instead of putting them back on my phone.  Apparently the only sync control I know syncs my blank Iphone to Itunes and deletes my backed up apps. 
How do I put my backed up apps back on my phone without losing them again?

I took the leap and tried to restore the backup of my apps from my second computer with Home XP to my Iphone but after the sync nothing shows up on my iphone.
I also had to completely reformat the harddrive on my Windows 7 computer and re-install all systems and Itunes.
Needless to say I don't like Itunes very much at all after this experience.  Not a very pleasant 24 hours for me,  to say the least,  and I still cannot get Itunes to re-install my lost apps to my iphone or any of my music or videos.
Can't say I am very impressed with iphone or Apple software either.
If anyone has the vaguest notion of what can be going on here I would appreciate some feedback,  as apparently Apple,  unlike Micorsoft,  does not offer that for free,  as far as I know.

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