Hi, I have two questions.

(A) Is there any software which can pull the list of current installed APPs from Iphone into a PC?
(B) Is there any software which can read this list to re-install all APPs in one push after restore new firmware and JB/Active/Unlock?

I am sure that millions of JB Iphone users will be very happy to use such a software to avoid manually re-install APPs one by one after upgraded to new firmware.

you could try using SSH to back up apps folder or iphone pc suite, those are my best guesses

I believe you will have to manually install the apps back to your iphone. I do not know any apps that does this in one push and maybe the reason is that, not all apps work on new fw so you'll have to select the apps that works with the new fw your iphone have. But I may be wrong. IMO

to add to what mr virus said installer might not recognize the apps so you might not be able to upgrade/uninstall them sadly enough