When you sync your iPad with your computer the data for that apps are backed up with the app. So if you loose your iPad you can just restore your new iPad from backup and be all set.
Besides what mentioned above, i like to share you a page about how to transfer iPod/iPhone/iPad to computer or iTunes, which included transferring iPad contents to computer/iTunes.
Hopefully this works for all of you like it just worked for me!
http://www.softwarebbs.com/wiki/IPod/iPhone/iPad_To_Computer_Transfer_%26_Backup_Software_Reviews

Transfer photos, music, videos from iPhone iPad iPod to computer or Mac

http://www.mustsoftware.com/Cucusoft-iPad-iPhone-iPod-to-Computer-Transfer-guide.html

For iphone/ipod/ipad to Mac transfer

http://www.recovery-iphone.com/ipod-iphone-to-mac-transfer.html

First reboot the iPad and then try syncing. If still unable to sync, make a backup (make sure your backup is current) and restore the device to it's factory setting and then restore from backup.

No it should save the data as well. For example like if you fb or aim if you sync your device and restore from back up you are still logged in to those accounts. I am pretty sure your fine but you may want to email the company of who ever made the app to be 100 percent sure.
More reviews:
For PC: How to sync data from iPad to PC
For Mac: How to sync data from iPad to Mac OS
It includes the transferring of music, photos, videos, SMS, Contact ect. between iPod/iPhone/iPad and computer(PC or Mac).

http://www.iphone-mac.com/how-to-transfer-and-sync-contents-from-ipad-to-pc.html
http://www.iphone-mac.com/how-to-transfer-and-sync-contents-from-ipad-to-mac.html

Yes I think the data can be transferred as well. When you plug your ipad into your computer, there should be a device on your desktop, just click to find your contents. The apps should be in in too. Choose those data you wanna transfer and then drag them to itunes or anywhere on your computer.
Of course you can also use [URL="http://www.levesoft.com/iPad-iPhone-iPod-to-computer-transfer.html[/URL] to move the data, it should save you a lot of time.

iphone backup&Recovery---You can free download or buy 20%~30% discout iphone backup&Recovery software in:

http://www.recovery-iphone.com