here is what i do :
the things u sync with ur itunes are safe
the only thing i need to backup for iphone that i dont sync with itunes is (for others iphones)
addressbook
notes
sms
bookmarks
can be found here
private/ var/ movile/ libraray/
( you can use disk aid to copy these folders to you computer and use diskaid again to put them back right there )
open diskaid and choose root folder from the bottom left corner
also u might want to copy all the images that u clicked on ur iphone to u computer
hope this is what u asked for 😛
good luck
note: i always prefer to setup iphone as a new phone after ever restore, this way u will have the latest preference files