Your iTunes backup of your 3GS that is created when you plug in your 3GS to your PC and sync/backup in iTunes does contain your calendar, notes and app data, and all of that is recreated when you restore. If you use Google and sync via Exchange than you can recreate your calendar and notes data that way... but that has nothing to do with app data.
Originally Posted by hassiman
Plu your 3GS in to iTunes and do a sync/backup (it doesn't matter if you have already activated the 4S and the 3GS no longer has your carrier active... it still will work). Then plug your new 4S in and at some point it will ask if you want to set up as new or restore from backup ... it will show you a drop-down list of backup files available. Pick the one you just completed and then wait for it to finish. If all goes well your 4S will then have everything your 3GS had and you are off and running... good luck!