A true backup

Can anyone advise on how to copy all apps, bought or otherwise, as well as cydia etc, before jailbreaking? I'm really frustrated with grabbing a ton of apps, setting up my iPhone really nice, only to have to lose everything when I chose to upgrade - like to 2.1 now.

It's a real hassle to start from scratch anytime Apple releases a new patch. I've heard about "chmod permissions" or something and copying files off my iPhone, pwning then copying them back once I'm done. Is this possible? And if so what are the steps?
I can't believe there's no way to keep everything you've worked hard to setup before upgrading.

Anybody? Thanks.

 

N E 1?