Since he's asking about an iPad, it should be noted that the "Transfer Purchased Items" method is the way it's supposed to be done, but I've had mixed results with that working in the real world.
When my wife and I just switched to the new VZ iPhones to change carriers, her Mac asked if it could do it, while mine didn't.
In her case, a number of Apps disappeared. I believe she may have gotten a few Apps purchased through my Apple Store account mixed into her iTunes library and had them on her phone. The feature only transfers back Apps associated with the Apple Store account that particular copy of iTunes is authorized against. (The others ended up in her Trash on her machine. They can be reinstalled by adding them back to her Library and making sure her machine is still authorized to play things from my Library. Apps are weird in that they're handled a like copy-protected music files in iTunes. One of the complaints levered against iTunes is that it tries to do too much, and in that -- I agree. I think they should split the device App installation and other things out of it, but they won't... it's too integrated in the iTunes Music Store... ahem, Apple App Store, which is really the same thing, under the hood.)
In my case, my two iPhones behave as if they have absolutely nothing in common and can both be plugged into my Mac, even though the VZ phone was restored from a backup of the AT&T one, and all the Apps and content were copied into the VZ device, just fine.
The real oddity was that iTunes lost the App layout (putting apps in "folders") from the original device even though it was a "restore from backup" and I ended up fixing all of that manually, staring at the old phone and moving things on the screen around to re-create the folders and get all the Apps back on the screens I wanted them in.
(Even though I have something like 100 Apps, there's only two "pages" active on my iPhone. The "folder" feature is used HEAVILY by me.)
So... then you get into the "alternate" methods of getting files off the iPhone/iPad, and those require jail breaking the device. I just don't go there. The bugs in Apple's supported stuff are plenty for me, without me having to go blow up the device at the command line... and this coming from someone who lives at the command-line all day for a living.
All in all... a backup/restore has always worked well for me from the Mac (or PC) back onto the same device, but in upgrades from iPhone 3 to iPhone 4, and from iPhone 4 AT&T to iPhone 4 VZ, things were always a little "wonky" in some way or another. Never has one of my iDevices "restored" from a backup of one to another or "upgraded", ever been "exactly right" after the reinstall. Something as simple as the folder locations being lost, or even a bad iOS upgrade once that required restoring the device to factory defaults, then restoring from a backup. It's always been "weird".
If it works, it's great. And if the hard disk dies in the host PC your iDevice is synced into... you really want backups of the machine to recover from. You want those anyway, so if you don't have a good bare-metal backup and recovery scheme for your PC, now's a good time to set one up.
Another thing I noted (I've seen this article before) that's important to note... on page 3 where they review 3rd Party Software to do this restore job, they're talking about iTunes 7. I'm currently on iTunes 10.4.1 on Mac, which shows how dated the article is.
Some of that stuff may not even be around, or may not have been updated to work on current versions of iTunes. Be careful. Looking at the comments, there's still some "success" messages into 2011, but they're lacking in detail of which recovery method they utilized. I suspect, they never had to go past the Apple restore-from-backup method on Page 1, but who knows?
These details are important, but to most it's just going to sound like us tech-heads actually like typing up all this seemingly "unimportant" stuff just to seem important, as one commenter to that article said.
Our brethren writing all the crazy never-ending code changes, force us into sounding like this... which sucks. Software is the ultimate moving target.
