The applications on your iPhone should actually transfer without any problems using the "Transfer Purchases From..." option in the File menu in iTunes. See if you can at least do that first. There is software to pull your music off your iPhone and put it into your iTunes library -
here's a recent thread on this with some recommendations.
EDIT: That thread talks about PC software, but a Mac equivalent is
PodWorks. I haven't used this one myself, but this is the type of application you can use...