Well, someone posted this in the comments as well:
Ok guys. I did 2nd Gen to 3.0 and I did it without losing any of my ipod files. I can only say this works for 2ND GEN ITOUCH TO 3.0 FINAL RELEASE. Here is what I did:
1. Download the 2nd gen 3.0 ispw file.
2. load up itunes.
3. plug in your itouch.
4. it will show up in your itunes. now on the main screen for it, there will be 2 options: “check for update” and “restore”
5. click on “check for update”. it will take you to the page where it says the features and says “buy for 9.99″ or “cancel”.
6. press the cancel button.
7. now it will return to the main page you were at, except this time it will say “update” instead of “check for update”
8. hold your shift key and left click “update”
9. double click the 3.0 file you downloaded.
10. let it run its course like normal.
wallah, you won’t have lost any files cuz it will treat it as an update and not a restore, and you will have a functioning 3.0 update. good luck folks.
Besides, can't you just backup you current apps and other settings *before* you upgrade?
It seems that if you do the "Hold Shift and Click UPDATE instead of RESTORE" thing, that should upgrade without restoring. make sure you have iTunes 8.2!