No it will not. Make sure you back up your phone in iTunes before you jailbreak just in case though. Use redsn0w to jailbreak and you will keep everything on your phone without having to do the whole restore/ restore from backup process.
Pwnage Tool requires a restore, which will erase the data. When you are done it will ask you if you want to restore to factory settings or from back up. Restoring from back can cause potential problems, so I recommend restoring to factory settings. You can easily sync your media, notes, apps etc back on in iTunes. Be sure to back up your contacts in a Google or Yahoo acct and sync them in iTunes before doing this if you don't have a mobile me account. You'll have to put your settings back in when you're done as well.
If you wait for the QuickPWN release, you won't need to restore the phone and the entire JB process will take less than 10 minutes. You will however have to restore the phone each time you want to do an Apple FW update. That to me is the biggest drawback to jailbreaking but it's still worth it IMO.
JB'b me and my wife's 3.0 3G iPhones with redsn0w.
(Due to a separate minor issue, had to JB mine twice)
Contacts and Calendar entries are in Outlook.
Ringtones, Music, Photos and Applications in iTunes.
After JB, only remaining task we had to do was to re-install
our favorite Cydia apps...
Fortunately, no issues or data lost...but your mileage may vary...