Restore PC, keep iTunes backup and iPhone backups - How to?

I would like to restore my PC back to factory settings.
I've once before transfered my iTunes Library from one to another computer and even restored it on my old desktop PC, though i had some problems...
--> most of my songs got little "?" in front of them and iTunes tells me it can't find them, which is really annoying cos i am not gonna put them all back in (45gb music is no fun...)
Is there any way i am too stupid to know to prevent that from happening?
But second of all and even more important is what will happen with my iPhone and my iTouch? All the Apps and all that stuff? I would like to keep my iPhone as it is but still restore my PC...is that possible?
Thanks a lot
and i really used the search before posting this but i just couldn't find the right answer. If I appear to be too lazy to open my eyes correctly it would still be nice if you would help me by posting the link ;-)

You may also find this Article of Interest...
Old Phone to New Phone
http://support.apple.com/kb/HT2109

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