Andrew Grant has a great write-up on how to sync your iPhone with two iTunes. I followed it and everything worked – at least almost.
There is one thing that he doesn’t remind you to do, which is quite important if you don’t want to lose your apps. Remember to authorize the new iTunes before syncing the first time!
I didn’t remember to authorize my new MacBook’s iTunes, so with the first sync I lost a majority of my apps. And then I screwed around with restoring and syncing with the old computer and lost data from my backups as well. Urgh.
Luckily most of the apps I use to store data automatically sync with various online services (Evernote, RTM etc.) My only real headache came from the several hours of lost audio notes, that I hadn’t synced onto a computer yet. And since I deleted the app and then resynced on both computers, I lost the data from the backups as well.
But if you ever need to extract data from a iPhone backup, I really recommend using Erica Sadun’s mdhelper. True, it’s a command line tool but I’m also a command line type of guy.