IPhone :: ITunes - Best Way To Sync Music And Apps Outside

After jailbreaking and getting my phone exactly the way I want it, I've decided I don't want to have to use iTunes to manage my music and Apps. I just reformatted my PC, and now iTunes wants me to totally wipe my iPhone and start over - this is unacceptable.

So I would like to manage my music outside of iTunes, but prefereably still using the iPod app as opposed to a third party one. I did a quick search and found nothing on the forums. Googling has led me to a few ideas, but they all seem dated. I am not familiar enough with SSH to figure this one out by myself.

Apps may be trickier, but there are a number of apps I have downloaded through Cydia, etc. that I would need to re-download if I wiped my phone.

Any tips or advice would be great here. Each successful thread I post takes me one step closer to leaving Big Brother out of my smartphone experience!